File Changes for wong
switch to commits view, user indexv265_base to v266_preview (2012-03-27 to 2012-04-10) v266
- src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf
- lines changed 1, context: html, text, full: html, text
incorrect assembly in daf for mouse
- src/hg/encode/encodeLoad/installSqlSchemas.pl
- lines changed 23, context: html, text, full: html, text
removed old bigBedTypes support (tagalign stuff), makes Tim's life easier
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/encode/encodeQaInit/encodeQaInit
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 1, context: html, text, full: html, text
added insertLength to the or None pile
- lines changed 5, context: html, text, full: html, text
corrected some syntax errors, and changed conditional on bedRnaElements to allow a dot in the 8th field
- lines changed 6, context: html, text, full: html, text
added in conditional to always use the sex from ddf regardless of if it's a tissue or not
- src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
- lines changed 10, context: html, text, full: html, text
some minor updates, changed how html is outputted, and all authors are used for alphabetizaio instead of just first
- lines changed 26, context: html, text, full: html, text
cleaned up the pubmed central path a bit
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- lines changed 6, context: html, text, full: html, text
changed variable name to be more descriptive, changed errors to print to stderr
- src/hg/encode/qaEncodeTracks2/qaEncodeTracks2
- lines changed 1, context: html, text, full: html, text
changed hashbang to new standard
- src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/encode/raDiff/raDiff
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/encode/raMerge/raMerge
- lines changed 1, context: html, text, full: html, text
changed hash bangs over to new styles
- src/hg/lib/bigBed.as
- lines changed 10, context: html, text, full: html, text
adding in dummy as and sql files for bigBed
- src/hg/lib/bigBed.sql
- lines changed 17, context: html, text, full: html, text
adding in dummy as and sql files for bigBed
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- lines changed 566, context: html, text, full: html, text
notes for caltech rna seq
- lines changed 566, context: html, text, full: html, text
reverting to b9fbbd2f2d1db6c0a26c06712148113494b962bc for release 2 notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release3.notes
- lines changed 1393, context: html, text, full: html, text
release notes for caltech release 3
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
- lines changed 3739, context: html, text, full: html, text
adding notes foir cshl long release 2
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromChip.release2.notes
- lines changed 122, context: html, text, full: html, text
updated notes files for open chrom chip
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release4.notes
- lines changed 739, context: html, text, full: html, text
adding in notes for histone and dgf
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release5.notes
- lines changed 2201, context: html, text, full: html, text
notes for uw dnase release 5
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release4.notes
- lines changed 2492, context: html, text, full: html, text
adding in notes for histone and dgf
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 8, context: html, text, full: html, text
addingin FSU mouse tiling platform
- lines changed 3, context: html, text, full: html, text
description and type got merged for DBA/2
- lines changed 4, context: html, text, full: html, text
added in and corrected some labels
- lines changed 1, context: html, text, full: html, text
correcting capitalization error
- lines changed 1, context: html, text, full: html, text
qa fixes, and more labels in cv fun
- lines changed 3, context: html, text, full: html, text
more label changes for qa
- lines changed 1, context: html, text, full: html, text
changed description at lab's behest
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 2676, context: html, text, full: html, text
added in new broad histone metaDb
- lines changed 2676, context: html, text, full: html, text
Errors in metaDb, not all submissions have an antibodyRevert "added in new broad histone metaDb"
This reverts commit 6b7478127796dadd417430b7c59ab17af25b3692.
- lines changed 2676, context: html, text, full: html, text
adding in new tracks for broad histone metaDb
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 1476, context: html, text, full: html, text
revoked data and added in replacement files
- lines changed 121, context: html, text, full: html, text
added expIds and accessiosn to caltech rnaseq
- lines changed 549, context: html, text, full: html, text
filling in the treatment = none holes
- lines changed 118, context: html, text, full: html, text
filling in holes for insert length (doesn't exist for non paired reads)
- lines changed 181, context: html, text, full: html, text
correcting date submitted and unrestricted
- lines changed 171, context: html, text, full: html, text
filled in holes for localization and rnaExtract
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 357, context: html, text, full: html, text
added in more cshl long tracks
- lines changed 357, context: html, text, full: html, text
added in metadata that i forgot to
- lines changed 391, context: html, text, full: html, text
added in md5sums for cshl long rna seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 2588, context: html, text, full: html, text
added in metadata for new cshl short tracks
- lines changed 852, context: html, text, full: html, text
added in new tracks for cshl short
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- lines changed 153, context: html, text, full: html, text
fixed md5sums after another resubmit of all the data
- lines changed 91, context: html, text, full: html, text
adding in dcc Accessions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 3082, context: html, text, full: html, text
adding in metadata for gisrnaper
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 877, context: html, text, full: html, text
added in new open chrom chip tracks
- lines changed 290, context: html, text, full: html, text
converted controlIds to dccaccession
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 1470, context: html, text, full: html, text
added in metadata for new cshl short tracks
- lines changed 5044, context: html, text, full: html, text
added in metadata for new riken cage tracks
- lines changed 446, context: html, text, full: html, text
added in riken cage metaData part 2
- lines changed 39, context: html, text, full: html, text
last time there was a replacement file that didn't get the v4
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 1179, context: html, text, full: html, text
added in new tracks for uw dgf
- lines changed 181, context: html, text, full: html, text
data came in with incorrect metadata, correcting
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 2551, context: html, text, full: html, text
added in new metadata for UwDnase tracks
- lines changed 409, context: html, text, full: html, text
added in more uw dnase tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 1221, context: html, text, full: html, text
added in emtadata for uwhistone new tracks
- lines changed 11, context: html, text, full: html, text
revoked old dataset, missed becuase the histone tag changed between releases h3k4 vs h3k04
- lines changed 11, context: html, text, full: html, text
incorrectly revoked, turns out the repleacement was missing the treatment in the name
- lines changed 11, context: html, text, full: html, text
revoked objects that were missing treatment names, resubmitting
- lines changed 255, context: html, text, full: html, text
added in replacement tracks
- lines changed 4, context: html, text, full: html, text
putting an experiment without a rep2 into the attic, lab doesn't think it'll ever get rep2
- lines changed 143, context: html, text, full: html, text
added in controls as accessions, we dont' have all of them yet
- lines changed 21, context: html, text, full: html, text
adding in known accessions and expids
- lines changed 51, context: html, text, full: html, text
added in more controlIds
- lines changed 101, context: html, text, full: html, text
added in accessions and expids
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
- lines changed 272, context: html, text, full: html, text
staging the expIds for 3 tracks to beta for a metadata update
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
- lines changed 180, context: html, text, full: html, text
staging the expIds for 3 tracks to beta for a metadata update
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
- lines changed 9, context: html, text, full: html, text
staging the expIds for 3 tracks to beta for a metadata update
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
adding in new caltech rnaSeq release3.ra
- lines changed 1, context: html, text, full: html, text
bypassing patch.ra for replicate fix, and just going forward with release 5.
- lines changed 2, context: html, text, full: html, text
adding in release4.ra for uwhistone
- lines changed 2, context: html, text, full: html, text
split off release4 trackDb ra for uwDgf
- lines changed 1, context: html, text, full: html, text
added in new tracks for uw dgf
- lines changed 1, context: html, text, full: html, text
cleaned up trackDb in cshl long
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
- lines changed 674, context: html, text, full: html, text
adding in broad histone trackDb tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release2.ra
- lines changed 549, context: html, text, full: html, text
removed bad signals from caltech rnaseq
- lines changed 524, context: html, text, full: html, text
added in replacement tracks for caltech rna seq
- lines changed 1033, context: html, text, full: html, text
reverting to 5a655dd525b84371e1e9c3326f741ce23e3e378a because it was really release 3
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
- lines changed 2050, context: html, text, full: html, text
adding in new caltech rnaSeq release3.ra
- lines changed 674, context: html, text, full: html, text
reworked long and short labels from previous release, also cleamed out commented lines
- lines changed 1, context: html, text, full: html, text
removed md5sum from filesort order
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
- lines changed 33, context: html, text, full: html, text
added in more cshl long tracks
- lines changed 33, context: html, text, full: html, text
re-added in tracks for cshl long rna-seq lost in the merge
- lines changed 157, context: html, text, full: html, text
cleaned up trackDb in cshl long
- lines changed 94, context: html, text, full: html, text
fixed autogenerated long labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
- lines changed 1424, context: html, text, full: html, text
added in new trackDb tracks for cshl short contigs and whatnot
- lines changed 3, context: html, text, full: html, text
didn't notice monocytes in the tier 3 cell lines, corrected
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
- lines changed 30, context: html, text, full: html, text
added in changes from lab
- lines changed 11, context: html, text, full: html, text
more html chagnes by lab
- lines changed 35, context: html, text, full: html, text
added in references to duke affy exon
- lines changed 5, context: html, text, full: html, text
qa fixes, and more labels in cv fun
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
- lines changed 3, context: html, text, full: html, text
qa fixes, and more labels in cv fun
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
- lines changed 2598, context: html, text, full: html, text
added in new tracks from gis
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
- lines changed 145, context: html, text, full: html, text
added in new open chrom chip tracks
- lines changed 66, context: html, text, full: html, text
reworked short and long labels that were too long, and made all chagnes consistent
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
- lines changed 3173, context: html, text, full: html, text
added in tracks to riken cage release3 for freeze
- lines changed 1, context: html, text, full: html, text
flippign the matrix around, because ther'es too many cell lines now
- lines changed 158, context: html, text, full: html, text
added in new riken release 3 tracks part 2
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
- lines changed 167, context: html, text, full: html, text
added in release notes and new html for uw dgf
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
- lines changed 1488, context: html, text, full: html, text
split off release4 trackDb ra for uwDgf
- lines changed 567, context: html, text, full: html, text
added in new tracks for uw dgf
- lines changed 1, context: html, text, full: html, text
added in treatment to the cv list
- lines changed 1, context: html, text, full: html, text
added in release notes and new html for uw dgf
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.patch.ra
- lines changed 4562, context: html, text, full: html, text
removing patch.ra, using release5.ra instead
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
- lines changed 132, context: html, text, full: html, text
copying over release 4 html to 5
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.ra
- lines changed 4562, context: html, text, full: html, text
copying over wgEncodeUwDnase to release5 trackDb
- lines changed 738, context: html, text, full: html, text
added in new tracks to trackDb
- lines changed 109, context: html, text, full: html, text
added in more uw dnase tracks
- lines changed 101, context: html, text, full: html, text
new long labels for uw dnase
- lines changed 510, context: html, text, full: html, text
short labels for uwDnase
- lines changed 7, context: html, text, full: html, text
changed wi30O to wi38, same thing, treatment was embedded in cell name
- lines changed 182, context: html, text, full: html, text
removed fdr 1%, as everything is fdr 1%
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.html
- lines changed 96, context: html, text, full: html, text
added in release notes and new html for uw histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.ra
- lines changed 5953, context: html, text, full: html, text
adding in release4.ra for uwhistone
- lines changed 301, context: html, text, full: html, text
added in metadata for new cshl short tracks
- lines changed 102, context: html, text, full: html, text
revoked old tracks, added in replacement tracks
- lines changed 1, context: html, text, full: html, text
added in release notes and new html for uw histone
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 3121, context: html, text, full: html, text
added in new mouse tracls
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 1172, context: html, text, full: html, text
added in new mouse metaDb for sydh tfbs
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
- lines changed 362, context: html, text, full: html, text
added in enw tracks for licr histone
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
- lines changed 146, context: html, text, full: html, text
added in tracks to sydh tfbs mm9 trackDb
- src/hg/utils/automation/Encode.pm
- lines changed 8, context: html, text, full: html, text
removed daf version check
- lines changed 1, context: html, text, full: html, text
removed old bigBedTypes support (tagalign stuff), makes Tim's life easier
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