File Changes for braney

v236_base to v237_preview (2010-07-20 to 2010-07-27) v237

• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 1, context: html, text, full: html, text
    look for *.bigWig instead of *.bw
  • lines changed 3, context: html, text, full: html, text
    special case type for bam index file
  • lines changed 1, context: html, text, full: html, text
    add .bai files to those included in the output files
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 19, context: html, text, full: html, text
    don't gzip BAM or bigWigs
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 13, context: html, text, full: html, text
    don't gzip BAM or bigWigs
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 3, context: html, text, full: html, text
    don't output a separate metadata line for bam index files
  • lines changed 18, context: html, text, full: html, text
    don't gzip BAM or bigWigs
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 15, context: html, text, full: html, text
    add some options to let some errors pass through
• src/hg/makeDb/doc/hg18.txt
  • lines changed 2, context: html, text, full: html, text
    add tiny piece of information about UCSF Brain Methyl since we don't have Ting's load info
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    change UCSF Brain Methyl table names
  • lines changed 27, context: html, text, full: html, text
    edits from Mary
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
  • lines changed 138, context: html, text, full: html, text
    take metadata out of trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    copy from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 1873, context: html, text, full: html, text
    copy from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 272, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 399, 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/wgEncodeCaltechRnaSeq.ra
  • lines changed 72, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 121, 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/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 16, 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/wgEncodeCshlShortRnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 33, 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/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 6, 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/wgEncodeGisRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 12, 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/wgEncodeHaibMethylSeq.ra
  • lines changed 44, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 44, 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/wgEncodeHaibTfbs.ra
  • lines changed 206, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 206, 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/wgEncodeOpenChromChip.ra
  • lines changed 59, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 118, 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/wgEncodeOpenChromDnase.ra
  • lines changed 66, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 122, 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/wgEncodeOpenChromFaire.ra
  • lines changed 31, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 61, 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/wgEncodeRikenCage.ra
  • lines changed 17, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 17, 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/wgEncodeSydhHistone.ra
  • lines changed 21, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 32, 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/wgEncodeSydhTfbs.ra
  • lines changed 452, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 489, 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/wgEncodeUwDgf.ra
  • lines changed 5, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 15, 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/wgEncodeUwDnase.ra
  • lines changed 72, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 144, 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/wgEncodeUwHistone.ra
  • lines changed 140, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 280, context: html, text, full: html, text
    change the fileName for BAMs and bigWigs to take out the .gz
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 92, context: html, text, full: html, text
    transfer hg18 page over to hg19...
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 65, context: html, text, full: html, text
    oops, this was supposed to be in there a while ago
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 119, context: html, text, full: html, text
    transfer hg18 page over to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 8, context: html, text, full: html, text
    fix up some of the metadata
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 5, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 10, context: html, text, full: html, text
    take .gz off bigWig and BAM files
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 23, context: html, text, full: html, text
    add fileIndex for BAM files
  • lines changed 51, context: html, text, full: html, text
    take .gz off bigWig and BAM files
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 58, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
  • lines changed 221, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
• src/hg/utils/gff3ToPsl/makefile
  • lines changed 22, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes
• src/hg/utils/gff3ToPsl/tests/README
  • lines changed 2, context: html, text, full: html, text
    take out spurious comment
  • lines changed 13, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt
  • lines changed 21329, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 1, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/input/locusNameAndSize.txt
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl and add some test files
• src/lib/gff3.c
  • lines changed 5, context: html, text, full: html, text
    add new utility, gff3ToPsl that converts GFF3 files with CIGARs in GAP attributes