Commits for braney
switch to files view, user index
v236_base to v237_preview (2010-07-20 to 2010-07-27) v237
- add tiny piece of information about UCSF Brain Methyl since we don't have Ting's load info
- src/hg/makeDb/doc/hg18.txt - lines changed 2, context: html, text, full: html, text
- change UCSF Brain Methyl table names
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 10, context: html, text, full: html, text
- look for *.bigWig instead of *.bw
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl - lines changed 1, context: html, text, full: html, text
- add fileIndex for BAM files
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 23, context: html, text, full: html, text
- add fileIndex for BAM files
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 272, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 72, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 206, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 59, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 66, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 17, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 21, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 452, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 72, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 140, context: html, text, full: html, text
- special case type for bam index file
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl - lines changed 3, context: html, text, full: html, text
- don't output a separate metadata line for bam index files
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 3, context: html, text, full: html, text
- add .bai files to those included in the output files
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl - lines changed 1, context: html, text, full: html, text
- take .gz off bigWig and BAM files
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 51, context: html, text, full: html, text
- copy from hg18
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra - lines changed 1873, context: html, text, full: html, text
- change the fileName for BAMs and bigWigs to take out the .gz
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 399, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 121, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 206, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 118, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 122, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 61, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra - lines changed 17, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra - lines changed 32, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 489, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 144, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 280, context: html, text, full: html, text
- don't gzip BAM or bigWigs
- src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 19, context: html, text, full: html, text
- src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 13, context: html, text, full: html, text
- src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 18, context: html, text, full: html, text
- edits from Mary
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 27, context: html, text, full: html, text
- add some options to let some errors pass through
- src/hg/encode/validateFiles/validateFiles.c - lines changed 15, context: html, text, full: html, text
- transfer hg18 page over to hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html - lines changed 119, context: html, text, full: html, text
- take metadata out of trackDb
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra - lines changed 138, context: html, text, full: html, text
- transfer hg18 page over to hg19...
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html - lines changed 92, context: html, text, full: html, text
- oops, this was supposed to be in there a while ago
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra - lines changed 65, context: html, text, full: html, text
- take out spurious comment
- src/hg/utils/gff3ToPsl/tests/README - lines changed 2, context: html, text, full: html, text
- fix gff3ToPsl and add some test files
- src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 58, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/README - lines changed 13, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt - lines changed 21329, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl - lines changed 1, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit - lines changed 0, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff - lines changed 7, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/input/locusNameAndSize.txt - lines changed 24, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/tests/makefile - lines changed 24, context: html, text, full: html, text
- fix up some of the metadata
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra - lines changed 8, context: html, text, full: html, text
- add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
- src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 221, context: html, text, full: html, text
- src/hg/utils/gff3ToPsl/makefile - lines changed 22, context: html, text, full: html, text
switch to files view, user index