Commits for wong

v255_base to v256_preview (2011-08-08 to 2011-08-16) v256

• fixed a message
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 1, context: html, text, full: html, text
• an unless turned into an if, i got a little too exited with the unless statements, resulted in a logic error. Everytime a md5sum last modified date existed, it would get 0 as it's last modified date, i wanted that for files that didn't exist the last time md5sum was ran only. an unless is equivalent to if not (if !(condition));
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 1, context: html, text, full: html, text
• changed verbosity level for some debugging prints\n
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 2, context: html, text, full: html, text
• fixed metadata errors
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra - lines changed 21, context: html, text, full: html, text
• fixed metadata issue
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 39, context: html, text, full: html, text
• revoked SL1196
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 16, context: html, text, full: html, text
• changed milli liters to microliters
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html - lines changed 1, context: html, text, full: html, text
• loaded new uw tracks
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 434, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 1405, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 619, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 361, context: html, text, full: html, text
• corrected some pre-QA errors
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 1, context: html, text, full: html, text
• one of the rows was missing treatment
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 2, context: html, text, full: html, text
• more treatment correction errors
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 2, context: html, text, full: html, text
• added one more submission 4696
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 9, context: html, text, full: html, text
• added functionality to put md5sum in metaDb
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 88, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 945, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 163, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 1243, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 145, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 215, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra - lines changed 74, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra - lines changed 405, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 168, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 1696, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 285, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 347, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 189, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 183, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 1839, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra - lines changed 136, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 811, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 956, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 732, context: html, text, full: html, text
• added in function to bot put bai in md5sum for bam if bai is missing
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 14, context: html, text, full: html, text
• previous commit bot = not, this one i removed a variable i didn't use
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 1, context: html, text, full: html, text
• added md5sums
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 171, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 186, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 259, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 341, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra - lines changed 116, context: html, text, full: html, text
• removed old comment from before we had design finalized
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 1, context: html, text, full: html, text
• corrected some md5 errors, there were colliding file names
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 2, context: html, text, full: html, text
• lots of changes, more fleshed out comments, and found some bugs, namely the multiple regex match bug. added functionality to detect file bas name collisions, for table lookup purposes.
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 303, context: html, text, full: html, text
• updated md5sums for colliding file names
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 5, context: html, text, full: html, text
• removed metadata lines
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra - lines changed 3, context: html, text, full: html, text
• renamed wgEncodeGencode.ra to wgEncodeGencodeV3.ra
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra - lines changed 55, context: html, text, full: html, text
• modified makefile
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• commented out multi view section
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html - lines changed 2, context: html, text, full: html, text
• changed sc582 > sc584, and added in new objects
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 25, context: html, text, full: html, text
• fixed html stuff and removed view settings from trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 7, context: html, text, full: html, text
• updated some md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra - lines changed 3, context: html, text, full: html, text
• made functionality to check if there if an existing metaDb entry per file, if there is no corresponding fileName entry, it assumes orphaned, and warns you. In addition to that, I added functionality to make an inverted hash of md5sums and file names to check if there are collisions with regards to md5sums.
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 25, context: html, text, full: html, text
• cleaned up gencode's references
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html - lines changed 2, context: html, text, full: html, text
• alphabetized references
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html - lines changed 9, context: html, text, full: html, text
• cleaned up references for gencode hg19
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html - lines changed 9, context: html, text, full: html, text
• something went wrong on the add last time
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 324, context: html, text, full: html, text
• forgot treatment group
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra - lines changed 36, context: html, text, full: html, text
• loaded last bits of sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 257, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 177, context: html, text, full: html, text
• updated the release2 notes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes - lines changed 448, context: html, text, full: html, text
• commented out k562b and hepg2b
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 36, context: html, text, full: html, text
• updated notes file for uw dnase and uw histone
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release3.notes - lines changed 217, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes - lines changed 255, context: html, text, full: html, text
• html correction per QA request
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• sydh tfbs html fixes at QA's request
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html - lines changed 5, context: html, text, full: html, text
• changed windowsing function to mean+whiskers
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 1, context: html, text, full: html, text
• forgot snyder is part of stanford now
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html - lines changed 1, context: html, text, full: html, text
• changed t-rex-hek293 to hek293-t-rex
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• changed t-rex-hek293 > hek293-t-rex and fetalpbde > pbdefetal
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 873, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 31, context: html, text, full: html, text
• changed fetalpbde to pdbefetal
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• inserted md5sums for new files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 19, context: html, text, full: html, text
• updated notes file for new files and name changes
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 2020, context: html, text, full: html, text
• added treatment as an expvar
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 1, context: html, text, full: html, text
• Merge branch 'validate'
• extra .txt extension in variable, removed from open statement
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 1, context: html, text, full: html, text