All File Changes

v257_base to v258_preview (2011-09-19 to 2011-09-27) v258

• build/crontabs/qateam/hgwbeta.crontab
  • lines changed 13, context: html, text, full: html, text
    Finally checking in the crontabs that belong to the qateam user, which we depend on for a lot. Redmine #404.
  • lines changed 13, context: html, text, full: html, text
    Moving the qateam crontab files to the genecats source tree instead. Thanks, Brian. (Redmine #404.)
• build/crontabs/qateam/hgwdev.crontab
  • lines changed 131, context: html, text, full: html, text
    Finally checking in the crontabs that belong to the qateam user, which we depend on for a lot. Redmine #404.
  • lines changed 131, context: html, text, full: html, text
    Moving the qateam crontab files to the genecats source tree instead. Thanks, Brian. (Redmine #404.)
• python/lib/ucscgenomics/cv.py
  • lines changed 21, context: html, text, full: html, text
    added first pass of documentation to cv and ra
• python/lib/ucscgenomics/ra.py
  • lines changed 65, context: html, text, full: html, text
    added first pass of documentation to cv and ra
  • lines changed 2, context: html, text, full: html, text
    more documentation for ucscgenomics
• python/lib/ucscgenomics/track.py
  • lines changed 41, context: html, text, full: html, text
    more documentation for ucscgenomics
• src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
  • lines changed 51, context: html, text, full: html, text
    Merging two DAFs
• src/hg/encode/DAFs/2.0/uwRepliSeq.daf
  • lines changed 72, context: html, text, full: html, text
    Added new terms to accomadate for Replication Timing data. Added the first draft of DAF for new composite.
  • lines changed 10, context: html, text, full: html, text
    Forgot 3 views. Checked in an incomplete DAF last time.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf
  • lines changed 79, context: html, text, full: html, text
    Added RepliSeq DAF update.
  • lines changed 8, context: html, text, full: html, text
    Updated DAF view name from Valley -> Valleys and removed longLabels.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechHistone.daf
  • lines changed 62, context: html, text, full: html, text
    Removed duplicate DAF to wgEncodeCaltechHist.daf.
• src/hg/encode/DAFs/3.0/mm9/wgEncodePsuHistone.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the version number that doesn't include longLabelPrefix's, to send to lab.
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 0, context: html, text, full: html, text
    changed whitespace structure
  • lines changed 15, context: html, text, full: html, text
    Patched encodeMkFilesList to special case the weirdo cellType>cell and Antibody>antibody weirdness
  • lines changed 910, context: html, text, full: html, text
    restructred encodeMkFilesList to be more like accepted conventions
  • lines changed 122, context: html, text, full: html, text
    rebuilt the md5sum > metaDb function to allow for comma delimited lists, also added a switch to go between a fast sql lookup with assumptions, and a robust one if that fails
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 4, context: html, text, full: html, text
    removed legacy code that append PI name if different than grant PI
• src/hg/encode/encodeValidate/newtest/DataBrowser.pm
  • lines changed 43, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/README
  • lines changed 1, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/out/README.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/out/load.ra
  • lines changed 27, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/out/mdb.txt
  • lines changed 3, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/out/trackDb.ra
  • lines changed 44, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/allGood/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/allGood/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/allGood/test.cfg
  • lines changed 3, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/hasReplicates/test.cfg
  • lines changed 5, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/test.cfg
  • lines changed 49, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredVar/test.cfg
  • lines changed 5, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/sunyGeneST.daf
  • lines changed 27, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfDafs/requiredView/test.cfg
  • lines changed 10, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/out/README.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/out/load.ra
  • lines changed 27, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/out/mdb.txt
  • lines changed 3, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/out/trackDb.ra
  • lines changed 44, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/badDdfs/fieldsMismatch/test.cfg
  • lines changed 6, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/README.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/load.ra
  • lines changed 18, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/mdb.txt
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/sunyGeneST.daf
  • lines changed 23, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/test.cfg
  • lines changed 3, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingAssembly/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingAssembly/test.cfg
  • lines changed 11, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingCompositesuffix/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingCompositesuffix/test.cfg
  • lines changed 6, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingDatatype/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingDatatype/test.cfg
  • lines changed 6, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingGrant/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingGrant/test.cfg
  • lines changed 10, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingGroup/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingGroup/test.cfg
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingLab/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingLab/test.cfg
  • lines changed 6, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingVariables/stanfordHg19Tfbs.daf
  • lines changed 35, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/missingVariables/test.cfg
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/out/README.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/out/load.ra
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/out/mdb.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/out/trackDb.ra
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/sunyGeneST.daf
  • lines changed 23, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/test.cfg
  • lines changed 3, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/cv.ra
  • lines changed 11173, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/downloadsReadmeTemplate.txt
  • lines changed 39, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/expVars.ra
  • lines changed 196, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/fields.ra
  • lines changed 419, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/hg18_chromInfo.txt
  • lines changed 49, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/labs.ra
  • lines changed 68, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/config/pi.ra
  • lines changed 181, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/doEncodeMock.pl
  • lines changed 28, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
  • lines changed 2409, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/ELAVL1_H1ESC_hg19_broadpeak.bed
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/ELAVL1_H1ESC_hg19_broadpeak.bed.00
  • lines changed 2874, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/ELAVL1_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/T7Tag_H1ESC_hg19_broadpeak.bed
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/T7Tag_H1ESC_hg19_broadpeak.bed.00
  • lines changed 147, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/T7Tag_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/input_H1ESC_hg19_broadpeak.bed
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/input_H1ESC_hg19_broadpeak.bed.00
  • lines changed 22855, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/input_H1ESC_hg19_broadpeak.bed.report
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/out/README.txt
  • lines changed 0, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/out/load.ra
  • lines changed 18, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/out/mdb.txt
  • lines changed 2, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/out/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
• src/hg/encode/encodeValidate/newtest/realone/sunyGeneST.daf
  • lines changed 22, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/realone/sunyGeneST.ddf
  • lines changed 4, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 0, context: html, text, full: html, text
    removed dos style carriage return in unit test dafs and ddfs
• src/hg/encode/encodeValidate/newtest/tester.pl
  • lines changed 150, context: html, text, full: html, text
    thought I added in the unit tests for encodeValidate earlier. This is the first draft. There are some kinks to work out, but I want to save them here now in case somethign goes wrong
  • lines changed 1, context: html, text, full: html, text
    commented out custom package
• src/hg/hgApi/hgApi.c
  • lines changed 4, context: html, text, full: html, text
    add defaultPos
  • lines changed 1, context: html, text, full: html, text
    add a missing else
• src/hg/hgGene/geneReviews.c
  • lines changed 53, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
  • lines changed 52, context: html, text, full: html, text
    Finished GeneReviews for UCSC knownGenes (hg19)
  • lines changed 3, context: html, text, full: html, text
    Finished geneReviews for OMIM genes
  • lines changed 9, context: html, text, full: html, text
    Finished up the bigBed update approach for geneReviews track
• src/hg/hgGene/hgGene.c
  • lines changed 3, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
  • lines changed 1, context: html, text, full: html, text
    Finished GeneReviews for UCSC knownGenes (hg19)
• src/hg/hgGene/hgGene.h
  • lines changed 4, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
  • lines changed 3, context: html, text, full: html, text
    Finished GeneReviews for UCSC knownGenes (hg19)
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    danRer6 becomes danRer7
• src/hg/hgGene/hgGeneData/section.ra
  • lines changed 5, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 7, context: html, text, full: html, text
    allow for appending to log files #5148
• src/hg/hgTracks/makefile
  • lines changed 18, context: html, text, full: html, text
    build hgRenderTracks as well as hgTracks (see redmine #4888)
• src/hg/hgTracks/makefile.hgRenderTracks
  • lines changed 22, context: html, text, full: html, text
    build hgRenderTracks as well as hgTracks (see redmine #4888)
• src/hg/hgc/hgc.c
  • lines changed 60, context: html, text, full: html, text
    initial geneReviews aork
  • lines changed 39, context: html, text, full: html, text
    Add geneReviews pointer to refSeq genes.
  • lines changed 32, context: html, text, full: html, text
    Finished add GeneReview GRShort links to refSeq gene's detail page.
  • lines changed 2, context: html, text, full: html, text
    hgGene, hgc, section.ra change for phase 2 of geneReviews track
  • lines changed 2, context: html, text, full: html, text
    Finished GeneReviews for UCSC knownGenes (hg19)
  • lines changed 29, context: html, text, full: html, text
    Finished geneReviews for OMIM genes
  • lines changed 6, context: html, text, full: html, text
    tint polish on geneReviews detail print out
  • lines changed 18, context: html, text, full: html, text
    Merge branch 'master' into geneReviews
  • lines changed 52, context: html, text, full: html, text
    Finished up the bigBed update approach for geneReviews track
  • lines changed 8, context: html, text, full: html, text
    Complete switch over to use bigBed trick
  • lines changed 11, context: html, text, full: html, text
    Cleaned out some debugging statements like fflush() etc.
  • lines changed 70, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    initial geneReviews aork
  • lines changed 3, context: html, text, full: html, text
    Add geneReviews pointer to refSeq genes.
  • lines changed 4, context: html, text, full: html, text
    Finished add GeneReview GRShort links to refSeq gene's detail page.
  • lines changed 1, context: html, text, full: html, text
    Finished geneReviews for OMIM genes
  • lines changed 6, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 17, context: html, text, full: html, text
    Added a note about adding track hubs directly to the browser URL to the 'Viewing Track Hubs' section. Changed the paragraph about hubCheck being available soon to reflect that hubCheck is now available.
• src/hg/htdocs/goldenPath/help/trackSearch.html
  • lines changed 17, context: html, text, full: html, text
    adding information about the free text and comma-separated list text fields in the track search help, redmine #5252
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 7, context: html, text, full: html, text
    Reduced author list on first pub, per Greg.
• src/hg/inc/hdb.h
  • lines changed 13, context: html, text, full: html, text
    Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19
  • lines changed 13, context: html, text, full: html, text
    Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19" This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.
• src/hg/inc/kgXref.h
  • lines changed 2, context: html, text, full: html, text
    Added an rfam accession field to the end of the kgXref table
  • lines changed 2, context: html, text, full: html, text
    Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
• src/hg/inc/mdb.h
  • lines changed 2, context: html, text, full: html, text
    Larry pointed out my bad spelling in code review. No actual logic change here.
• src/hg/js/ddcl.js
  • lines changed 1, context: html, text, full: html, text
    added var to a variable to amke it local
• src/hg/js/hgTracks.js
  • lines changed 34, context: html, text, full: html, text
    keep what the user last was looking at in view after in-place updates; fix stuff discovered via use strict (e.g. undeclared variables)
  • lines changed 30, context: html, text, full: html, text
    add code to support experimental UI work (redmine #5422)
• src/hg/js/jquery.watermarkinput.js
  • lines changed 81, context: html, text, full: html, text
    add jquery.watermarkinput.js
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    add jquery.watermarkinput.js
• src/hg/lib/geneReviewsBB.sql
  • lines changed 5, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/lib/geneReviewsBed5.as
  • lines changed 9, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/lib/geneReviewsRefGene.sql
  • lines changed 7, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/lib/genomicSuperDups.as
  • lines changed 1, context: html, text, full: html, text
    Corrected description of otherSize col of genomicSuperDups table.
• src/hg/lib/hdb.c
  • lines changed 38, context: html, text, full: html, text
    Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19
  • lines changed 38, context: html, text, full: html, text
    Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19" This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.
• src/hg/lib/hgBam.c
  • lines changed 2, context: html, text, full: html, text
    Samtools CIGAR strings have two new opcodes: '=' for exactly matchingbases, 'X' for mismatching bases. These are more explicit versions of the 'M' opcode for matching and/or mismatching bases.
• src/hg/lib/kgXref.as
  • lines changed 1, context: html, text, full: html, text
    Added an rfam accession field to the end of the kgXref table
  • lines changed 1, context: html, text, full: html, text
    Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
• src/hg/lib/kgXref.c
  • lines changed 11, context: html, text, full: html, text
    Added an rfam accession field to the end of the kgXref table
  • lines changed 10, context: html, text, full: html, text
    Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
• src/hg/lib/kgXref.sql
  • lines changed 15, context: html, text, full: html, text
    Added an rfam accession field to the end of the kgXref table
  • lines changed 1, context: html, text, full: html, text
    Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
  • lines changed 9, context: html, text, full: html, text
    Replaced key declarations that had been lost when I added the tRNA and rfam fields
• src/hg/lib/mdb.c
  • lines changed 11, context: html, text, full: html, text
    Larry pointed out my bad spelling in code review. No actual logic change here.
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 73, context: html, text, full: html, text
    starting xenTro3 lastz
  • lines changed 42, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 57, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release2.notes
  • lines changed 272, context: html, text, full: html, text
    Added Fixed release notes file. Fixes issue Redmine #4995.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release1.notes
  • lines changed 163, context: html, text, full: html, text
    Changed a few labels for Kate and generated a new notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 15, context: html, text, full: html, text
    Adjusting the notes file and the attic to not have tables for attic
  • lines changed 212, context: html, text, full: html, text
    Removing the 15 tables from the attic and changing bedRrbs to bed
  • lines changed 899, context: html, text, full: html, text
    hand generated notes file that takes into account renames, revokes, attic
  • lines changed 1, context: html, text, full: html, text
    Removed errant i
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 1309, context: html, text, full: html, text
    fixed notes file, removed extraneous warnings
• src/hg/makeDb/doc/galGal3.txt
  • lines changed 56, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
• src/hg/makeDb/doc/hg18.txt
  • lines changed 74, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/hg/makeDb/doc/hg19.txt
  • lines changed 56, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
  • lines changed 165, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
  • lines changed 13, context: html, text, full: html, text
    Rebuilt genomicSuperDups using corrected data.
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 53, context: html, text, full: html, text
    starting xenTro3 lastz
  • lines changed 11, context: html, text, full: html, text
    xenTro3 lastz finished
• src/hg/makeDb/doc/mm9.txt
  • lines changed 54, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
  • lines changed 10, context: html, text, full: html, text
    Rebuilt genomicSuperDups based on corrected data from provider.
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 57, context: html, text, full: html, text
    starting lastz on xenTro3
  • lines changed 8, context: html, text, full: html, text
    done with lastz chain net runs for xenTro3
• src/hg/makeDb/doc/proteins/101005.txt
  • lines changed 12, context: html, text, full: html, text
    Final commit of these scripts before the superuser sections get run - w00t
• src/hg/makeDb/doc/rn4.txt
  • lines changed 37, context: html, text, full: html, text
    starting lastz on xenTro3
  • lines changed 22, context: html, text, full: html, text
    xenTro3 lastz chain net completed
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 55, context: html, text, full: html, text
    (1) Updated the genomes and files used for buidling the *BlastTabs tables. (2) fixed a bug: the fold UTR tables were being built off not the temporary database but the current database (i.e. the released version). (3) Cleaned up some scripts to run the pfam jobs with pfam on /hive/scratch, where it shouldn't have as much adverse effects on the rest of the filesystem
  • lines changed 10, context: html, text, full: html, text
    Reviewed the databases and files to use for building the *BlastTab tables with Brooke. Revised some versions of some files to ensure that I'm building with the latest version to be released on the RR
  • lines changed 37, context: html, text, full: html, text
    Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19
  • lines changed 37, context: html, text, full: html, text
    Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19" This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.
  • lines changed 9, context: html, text, full: html, text
    Final commit of these scripts before the superuser sections get run - w00t
• src/hg/makeDb/doc/xenTro2.txt
  • lines changed 18, context: html, text, full: html, text
    adding liftOver to xenTro3
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 2, context: html, text, full: html, text
    adding ending marker after section
  • lines changed 121, context: html, text, full: html, text
    running lastz xenTro3 vs. these others
  • lines changed 71, context: html, text, full: html, text
    done with lastz chain net runs for xenTro3
• src/hg/makeDb/genbank/src/ccds/ccdsDownloadStep
  • lines changed 1, context: html, text, full: html, text
    NCBI's ftp server changed and so our regular expression needs to change.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 4, context: html, text, full: html, text
    Separator misspelled.
• src/hg/makeDb/trackDb/blastHg16KG.html
  • lines changed 1, context: html, text, full: html, text
    Removed italics around organism name variable. This file used by several organisms and some do not use binomial nomenclature.
  • lines changed 1, context: html, text, full: html, text
    Removed italics around organism name variable. This file used by several organisms and some do not use binomial nomenclature.
• src/hg/makeDb/trackDb/cow/bosTau2/gold.html
  • lines changed 4, context: html, text, full: html, text
    Made minor formatting changes
• src/hg/makeDb/trackDb/cow/bosTau3/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made some minor formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau3/gold.html
  • lines changed 4, context: html, text, full: html, text
    Make some minor grammatical/formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau4/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau4/gold.html
  • lines changed 4, context: html, text, full: html, text
    Made minor formatting/grammatical corrections
• src/hg/makeDb/trackDb/cow/bosTau5/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau5/gold.html
  • lines changed 4, context: html, text, full: html, text
    Made minor formatting/grammatical corrections
• src/hg/makeDb/trackDb/cow/bosTau6/ctgPos2.html
  • lines changed 2, context: html, text, full: html, text
    Changed the format of the text for the NCBI link. Removed an unnecessary period.
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
  • lines changed 5, context: html, text, full: html, text
    Made minor grammatical/formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau6/gold.html
  • lines changed 5, context: html, text, full: html, text
    Made some minor formatting/grammatical changes. Italicized 'Bos taurus'.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 62, context: html, text, full: html, text
    Added new terms to accomadate for Replication Timing data. Added the first draft of DAF for new composite.
  • lines changed 73, context: html, text, full: html, text
    Merge branch 'master' into UwReliSeq
  • lines changed 1, context: html, text, full: html, text
    changed regex for objStatus to accept renamed replaced or revoked with an explanation
  • lines changed 2, context: html, text, full: html, text
    corrected tags gor ifng
  • lines changed 1, context: html, text, full: html, text
    changed objStatus to be cvDefined No
  • lines changed 3, context: html, text, full: html, text
    TCF4 is now known as TCF7L2
  • lines changed 1, context: html, text, full: html, text
    changed monocytes's entry to reflect toher donor's scheme
  • lines changed 21, context: html, text, full: html, text
    re entered a non donored CD14+ cell line, as it is being used by other tracks, not sure if those tracks are from the donor or not
  • lines changed 1, context: html, text, full: html, text
    changed regex scheme of md5sum to match any amount of a comma delimited list of 32 length hex digits. testes against 1,2,3 terms in console's BRE, not in metaDb though.
  • lines changed 58, context: html, text, full: html, text
    Labelling changes already reviewed by Kate
  • lines changed 1, context: html, text, full: html, text
    Deprecating use of Astrocy as this is duplicated by NH-A. Redmine #4495.
  • lines changed 1, context: html, text, full: html, text
    made donored cd14+'s tag different than normal cd14+
• src/hg/makeDb/trackDb/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made some minor formatting changes
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 5, context: html, text, full: html, text
    Made minor grammatical changes. Changed formatting of textbook reference. Journal link pointed to dx.doi.org, but was redirected to ScienceDirect. Changed the link to go straight to ScienceDirect.
  • lines changed 1, context: html, text, full: html, text
    Removed capitalization from journal article title
• src/hg/makeDb/trackDb/gold.html
  • lines changed 4, context: html, text, full: html, text
    Made some minor grammatical corrections
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 46, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
  • lines changed 18, context: html, text, full: html, text
    minor touch up
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 38, context: html, text, full: html, text
    Updated the knownGene track description page to reflect the changes in content
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 326, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 327, context: html, text, full: html, text
    Updating md5sums
  • lines changed 359, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 96, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 97, context: html, text, full: html, text
    Updating md5sums
  • lines changed 96, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 119, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 120, context: html, text, full: html, text
    Updating md5sums
  • lines changed 119, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 62, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 63, context: html, text, full: html, text
    Updating md5sums
  • lines changed 66, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 51, context: html, text, full: html, text
    Added new release to fix Astrocy -> NH-A naming problem. Redmine #4995.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 29, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
  • lines changed 758, context: html, text, full: html, text
    Trying to add the new Chia PET data
  • lines changed 587, context: html, text, full: html, text
    Resolving merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 7, context: html, text, full: html, text
    Updating md5sums
  • lines changed 6, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 13, context: html, text, full: html, text
    Mostly changes around separateing GM12878 Cytosol rep 1 and rep2 into free and based
  • lines changed 21, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 22, context: html, text, full: html, text
    Updating md5sums
  • lines changed 21, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 5, context: html, text, full: html, text
    Updating md5sums
  • lines changed 4, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    Updating md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 14, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 51, context: html, text, full: html, text
    Adjusting the notes file and the attic to not have tables for attic
  • lines changed 203, context: html, text, full: html, text
    Changed the bedRrbs to bed
  • lines changed 2449, context: html, text, full: html, text
    Resolving merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 43, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 44, context: html, text, full: html, text
    Updating md5sums
  • lines changed 44, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 42, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 43, context: html, text, full: html, text
    Updating md5sums
  • lines changed 42, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 4005, context: html, text, full: html, text
    loaded lots of haib submissions
  • lines changed 177, context: html, text, full: html, text
    added md5sums for new files
  • lines changed 8, context: html, text, full: html, text
    added explanation to revoked status
  • lines changed 493, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 494, context: html, text, full: html, text
    Updating md5sums
  • lines changed 493, context: html, text, full: html, text
    added bai files to the fileName field
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 81, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 82, context: html, text, full: html, text
    Updating md5sums
  • lines changed 81, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 111, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 112, context: html, text, full: html, text
    Updating md5sums
  • lines changed 111, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 52, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 53, context: html, text, full: html, text
    Updating md5sums
  • lines changed 160, context: html, text, full: html, text
    Updated track to be consitent and renamed Astrocy -> NH-A. Redmine #4495, Redmine #4142.
  • lines changed 8, context: html, text, full: html, text
    Fixed spelling error of NH-A as NH-a.
  • lines changed 54, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 69, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 70, context: html, text, full: html, text
    Updating md5sums
  • lines changed 69, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 2, context: html, text, full: html, text
    md5sum was update when tested mkFilesList
  • lines changed 24, context: html, text, full: html, text
    Changed the V2 to reflect katrinas request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 16, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 17, context: html, text, full: html, text
    Updating md5sums
  • lines changed 16, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 1, context: html, text, full: html, text
    fixed SydhHistone (series not correctly updated)
  • lines changed 1, context: html, text, full: html, text
    fixed SydhTfbs too, and fixed the magic # for histone
  • lines changed 38, context: html, text, full: html, text
    Remove bam= and bai=
  • lines changed 1, context: html, text, full: html, text
    Updating md5sums
  • lines changed 36, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 20, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 21, context: html, text, full: html, text
    Updating md5sums
  • lines changed 20, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 5, context: html, text, full: html, text
    Updating md5sums
  • lines changed 4, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    fixed SydhTfbs too, and fixed the magic # for histone
  • lines changed 653, context: html, text, full: html, text
    Remove bam= and bai=
  • lines changed 961, context: html, text, full: html, text
    added in a lot of new submissions
  • lines changed 1, context: html, text, full: html, text
    Updating md5sums
  • lines changed 28, context: html, text, full: html, text
    changed some controls around and changed harvard to yale
  • lines changed 714, context: html, text, full: html, text
    added bai files to the fileName field
  • lines changed 66, context: html, text, full: html, text
    changed some control to be point to a expId instead of old method
  • lines changed 13, context: html, text, full: html, text
    corrected a mistake where a lab name was changed
  • lines changed 13, context: html, text, full: html, text
    more lab name changes
  • lines changed 103, context: html, text, full: html, text
    added expIds and dccAccessions
  • lines changed 10, context: html, text, full: html, text
    corrected one more controlId
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 28, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 28, context: html, text, full: html, text
    Updating md5sums
  • lines changed 28, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 1, context: html, text, full: html, text
    Updating md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 19, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 20, context: html, text, full: html, text
    Updating md5sums
  • lines changed 19, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 162, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 163, context: html, text, full: html, text
    Updating md5sums
  • lines changed 163, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 211, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 212, context: html, text, full: html, text
    Updating md5sums
  • lines changed 211, context: html, text, full: html, text
    cleaned up bam,bai fileName added md5sums
  • lines changed 793, context: html, text, full: html, text
    added in a new UW histone tracks (ones with donors)
  • lines changed 4, context: html, text, full: html, text
    changed replicate number
  • lines changed 793, context: html, text, full: html, text
    full reversiona s some donor id's were broken
  • lines changed 793, context: html, text, full: html, text
    added new tracks to TFBS and Histone, this time with corret donor ID's
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 169, context: html, text, full: html, text
    removed all bam= and bai=, leaving only a comma'd list of md5sums. mkFilesList still needs modifications to handle this
  • lines changed 170, context: html, text, full: html, text
    Updating md5sums
  • lines changed 377, context: html, text, full: html, text
    added some tracks, cleaned up bam,bai names in fileName
  • lines changed 377, context: html, text, full: html, text
    reverted to earlier tfbs after some loading errors
  • lines changed 208, context: html, text, full: html, text
    added new tracks to TFBS and Histone, this time with corret donor ID's
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 9884, context: html, text, full: html, text
    adding updated metaDb for HAIB Methyl RRBS, redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 622, context: html, text, full: html, text
    staging release 2 on beta, redmine #4834
  • lines changed 26, context: html, text, full: html, text
    pushing metadb updates to beta: matt fixed an md5sum and cricket expanded on the reason for the V2
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 343, context: html, text, full: html, text
    adding Matts updated metaDb, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Use wiki bigBed file trick to do automatic geneReviews update for hg19
  • lines changed 10, context: html, text, full: html, text
    Finished up the bigBed update approach for geneReviews track
  • lines changed 2, context: html, text, full: html, text
    Changed so that altSeqComposite (GRC patch 5) would show rather than patch2 on the RR.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 8, context: html, text, full: html, text
    added in .new.ra for openchrom synth, and since it is a one view track, Tim took out the view= tags
  • lines changed 2, context: html, text, full: html, text
    Added new release to fix Astrocy -> NH-A naming problem. Redmine #4995.
  • lines changed 2, context: html, text, full: html, text
    staging release 2 on beta, redmine #4834
  • lines changed 2, context: html, text, full: html, text
    staging HAIB Methy RRBS on hgwbeta, redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
  • lines changed 100, context: html, text, full: html, text
    Added new release to fix Astrocy -> NH-A naming problem. Redmine #4995.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.ra
  • lines changed 905, context: html, text, full: html, text
    Added new release to fix Astrocy -> NH-A naming problem. Redmine #4995.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 6, context: html, text, full: html, text
    fix up GENCODE findSpecs #5158
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 220, context: html, text, full: html, text
    Trying to add the new Chia PET data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 11, context: html, text, full: html, text
    Mostly changes around separateing GM12878 Cytosol rep 1 and rep2 into free and based
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 24, context: html, text, full: html, text
    Mostly changes around separateing GM12878 Cytosol rep 1 and rep2 into free and based
  • lines changed 9, context: html, text, full: html, text
    Changed a few labels for Kate and generated a new notes file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 762, context: html, text, full: html, text
    loaded lots of haib submissions
  • lines changed 721, context: html, text, full: html, text
    corrected a casing error made by alst commit
  • lines changed 2, context: html, text, full: html, text
    found another casing error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 13, context: html, text, full: html, text
    Updated track to be consitent and renamed Astrocy -> NH-A. Redmine #4495, Redmine #4142.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.new.ra
  • lines changed 196, context: html, text, full: html, text
    added in .new.ra for openchrom synth, and since it is a one view track, Tim took out the view= tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html
  • lines changed 4, context: html, text, full: html, text
    adding the fix of the scores to the release notes, redmine 4834
  • lines changed 2, context: html, text, full: html, text
    Changing description of the p-Value
  • lines changed 5, context: html, text, full: html, text
    removing reference to view since this is a single view track, fixed typo, grammar fix, fixed broken link, redmine #4834
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 13, context: html, text, full: html, text
    adding canPack and playing with composite settings to see why boxedCfg and pack is not working
  • lines changed 1, context: html, text, full: html, text
    commenting out minGrayLevel, which makes the min gray level configurable in hgTrackUi, because it works on dev but not on beta yet; on beta, with this setting, there is no gray-scale at all - all items are black, redmine #4834
  • lines changed 1, context: html, text, full: html, text
    adding the origAssembly hg18 to the parent stanza track because this track was actually lifted from hg18 and I want to reinstate the notice that was on the hgTrackUi page in the first release.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 14, context: html, text, full: html, text
    unrevoked an experiment for release2 that we still have no control for
  • lines changed 131, context: html, text, full: html, text
    added in a lot of new submissions
  • lines changed 2, context: html, text, full: html, text
    changed html code on some factors, and changed an input to be consistent with the control
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    changed some dimension names and other stuff in trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 2, context: html, text, full: html, text
    Attempted to turn on score filters for this track in response to Katrina's question (#92) in Redmine Track #141. This attempt was to no avail: I still see no score filters
  • lines changed 2, context: html, text, full: html, text
    Changed the default score filter
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    Attempted to turn on score filters for this track in response to Katrina's question (#92) in Redmine Track #141. This attempt was to no avail: I still see no score filters
  • lines changed 1, context: html, text, full: html, text
    fix to make the score ui appear
  • lines changed 1, context: html, text, full: html, text
    Changed the default score filter
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 246, context: html, text, full: html, text
    added in a new UW histone tracks (ones with donors)
  • lines changed 246, context: html, text, full: html, text
    full reversiona s some donor id's were broken
  • lines changed 246, context: html, text, full: html, text
    added new tracks to TFBS and Histone, this time with corret donor ID's
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 26, context: html, text, full: html, text
    added in 3 new tracks
  • lines changed 3, context: html, text, full: html, text
    addeed treatment lines
  • lines changed 26, context: html, text, full: html, text
    full reversiona s some donor id's were broken
  • lines changed 28, context: html, text, full: html, text
    added new tracks to TFBS and Histone, this time with corret donor ID's
• src/hg/makeDb/trackDb/human/omimDescriptionText.html
  • lines changed 15, context: html, text, full: html, text
    Made the box around the special note look nicer, and also match the note box on the DECIPHER track. Cleaned up some html formatting.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    initial geneReviews aork
  • lines changed 11, context: html, text, full: html, text
    To resolve merge conflict
  • lines changed 1, context: html, text, full: html, text
    Use green for geneReviews item
  • lines changed 4, context: html, text, full: html, text
    Finished up the bigBed update approach for geneReviews track
  • lines changed 2, context: html, text, full: html, text
    Complete switch over to use bigBed trick
  • lines changed 11, context: html, text, full: html, text
    Add geneReview track using database table approach
  • lines changed 10, context: html, text, full: html, text
    Disable geneReview track using database table approach
  • lines changed 1, context: html, text, full: html, text
    move geneReviews track into group phenDis from group X
• src/hg/makeDb/trackDb/microsat.html
  • lines changed 4, context: html, text, full: html, text
    Made minor grammatical changes. Inserted a link to the Tandem Repeats Finder as exists in the Simple Repeats track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 13, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
  • lines changed 426, context: html, text, full: html, text
    Added 5 controls missing from Histone track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 30, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 61, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 21, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 37, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 87, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 69, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 24, context: html, text, full: html, text
    Modifying md5sums to have no bam= or bai=
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
  • lines changed 1, context: html, text, full: html, text
    Added no inherint on so that Signal tracks would show in browser.
  • lines changed 46, context: html, text, full: html, text
    Added 5 controls missing from Histone track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Added no inherint on so that Signal tracks would show in browser.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 1, context: html, text, full: html, text
    adding a word that Katrina felt should be there in my code review, redmine#5365
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 4, context: html, text, full: html, text
    Made minor grammatical/formatting corrections
  • lines changed 1, context: html, text, full: html, text
    Inserted the word 'the' to correct a sentence structure
  • lines changed 2, context: html, text, full: html, text
    Corrected citation of Repeat Masker web site according to the FAQ on their site
  • lines changed 2, context: html, text, full: html, text
    Moved the dates for the Repeat Masker citation to the end of the line
  • lines changed 1, context: html, text, full: html, text
    Removed an unnecessary comma
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    Corrected citation of Repeat Masker web site according to the FAQ on their site
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    Added Robert Hubley to the Credits section as in the Interrupted Repeats track
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    Moved the dates for the Repeat Masker citation to the end of the line
• src/hg/makeDb/trackDb/sacCer/mrna.html
  • lines changed 2, context: html, text, full: html, text
    Edited slightly for grammar/accuracy.
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
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    Fixed some minor punctuation and formatting.
• src/hg/makeDb/trackDb/sacCer/sacCer3/sgdOther.html
  • lines changed 12, context: html, text, full: html, text
    Fixed broken link to the data file and reoranized and formatted text for better flow/readability
• src/hg/makeDb/trackDb/sacCer/transRegCode.html
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    Removed hyphen from 'well conserved'.
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to NCBI project page
• src/hg/makeDb/trackDb/simpleRepeat.html
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    Removed a comma before 'which'
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    The journal article URL was being redirected to a new URL. Replaced the existing URL with the direct URL.
• src/hg/makeDb/trackDb/tagTypes.tab
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    Attempted to turn on score filters for this track in response to Katrina's question (#92) in Redmine Track #141. This attempt was to no avail: I still see no score filters
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    adding xenTro3 chain net
• src/hg/makeDb/trackDb/turkey/melGal1/gap.html
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    Made some minor formatting corrections
• src/hg/makeDb/trackDb/turkey/melGal1/gold.html
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    Made minor grammatical corrections
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
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    better searches for gold and ctgPos2 tables
• src/hg/makeDb/trackDb/windowmaskerSdust.html
  • lines changed 1, context: html, text, full: html, text
    Made a minor grammatical correction
• src/hg/makeDb/trackDb/xenTro/xenTro1/gap.html
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    Made some minor grammatical corrections and a verb tense correction
• src/hg/makeDb/trackDb/xenTro/xenTro2/gap.html
  • lines changed 3, context: html, text, full: html, text
    Made some minor grammatical corrections
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    Made a verb tense correction
• src/hg/makeDb/trackDb/xenTro/xenTro3/gap.html
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    Italicized X. tropicalis
• src/hg/makeDb/trackDb/xenTro/xenTro3/gold.html
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    Made some formatting changes
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
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    better gold fragment name search
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    allow ctgPos2 search to find the chrM contig name too
• src/hg/oneShot/doOmimGene2/doOmimGene2.c
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    Replace mim2gene table with omim2gene table.
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    Added another ordering condition to reduce genes jumping around.
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    Added another ordering condition to reduce genes jumping around.
• src/hg/rnaStructure/utrFa/utrFa.c
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    Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19
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    Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19" This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.
• src/hg/txGene/txGeneXref/txGeneXref.c
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    Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
• src/hg/utils/automation/buildOmimTracks.csh
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    Checking in automation scripts for OMIM tracks.
• src/hg/utils/automation/checkBlastTabs.sh
  • lines changed 98, context: html, text, full: html, text
    initial source checks all dbs blast tabs
• src/hg/utils/automation/checkOmim.sh
  • lines changed 129, context: html, text, full: html, text
    Checking in automation scripts for OMIM tracks.
• src/hg/utils/cpAndLinkToResourceFiles.pl
  • lines changed 5, context: html, text, full: html, text
    restore functionality of copying over a non-versioned copy on production machines b/c these are used by static files
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    make sure file exists before deleting it (can happen b/c of loop over two destFiles)
• src/inc/bamFile.h
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    Samtools CIGAR strings have two new opcodes: '=' for exactly matchingbases, 'X' for mismatching bases. These are more explicit versions of the 'M' opcode for matching and/or mismatching bases.
• src/lib/bamFile.c
  • lines changed 8, context: html, text, full: html, text
    Samtools CIGAR strings have two new opcodes: '=' for exactly matchingbases, 'X' for mismatching bases. These are more explicit versions of the 'M' opcode for matching and/or mismatching bases.
• src/product/README.trackDb
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    clarify the relationship between db table name and track definition in the .ra file
• src/utils/geneReviews/addGeneReviewToBed.pl
  • lines changed 53, context: html, text, full: html, text
    Finished geneReviews for hg19 and hg18
• src/utils/qa/checkGbdbDiffs.csh
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    Simplified checkGbdbDiffs.csh so that it looks for missing files in all of /gbdb instead of a subset. This was prompted by a daily cron job error on an assembly with an entry in the dbDb table but no matching /gbdb directory. Removing getGbdbBeta.csh, as it was only called by checkGbdbDiffs.csh. Read more of my ramblings in Redmine #402.
• src/utils/qa/getGbdbBeta.csh
  • lines changed 110, context: html, text, full: html, text
    Simplified checkGbdbDiffs.csh so that it looks for missing files in all of /gbdb instead of a subset. This was prompted by a daily cron job error on an assembly with an entry in the dbDb table but no matching /gbdb directory. Removing getGbdbBeta.csh, as it was only called by checkGbdbDiffs.csh. Read more of my ramblings in Redmine #402.
• src/utils/qa/makefile
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    Removed getGbdbBeta.csh from git, so it also needs to be removed from makefile.
• src/utils/qa/weeklybld/buildEnv.csh
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    v258 preview1
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    comply with Brooke's request! #5148

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• files changed: 544