Commits for angie

v242_preview to v242_base (2010-10-05 to 2010-10-12) v242

• Added -tab option to bedIntersect (chopping by spaces, printing out w/tabs caused incorrect column counts).
  • src/hg/bedIntersect/bedIntersect.c - lines changed 5, context: html, text, full: html, text
• Removing redundant chomp's noticed by Belinda in code review.
  • src/hg/makeDb/doc/mm9.txt - lines changed 2, context: html, text, full: html, text
• Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
  • src/hg/bedIntersect/bedIntersect.c - lines changed 132, context: html, text, full: html, text
  • src/hg/bedIntersect/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/expected/aHitAny.aBigBSub.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.10.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.100.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.5.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.50.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.100.bed - lines changed 5, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.50.bed - lines changed 7, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.100.bed - lines changed 5, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.5.bed - lines changed 7, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.50.bed - lines changed 7, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/expected/allowStartEqEnd.aBigBSub.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/expected/allowStartEqEnd.aSubBBig.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAny.aBigBSub.bed - lines changed 1, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAny.aSubBBig.bed - lines changed 10, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAnyPlusBScore.aBigBSub.bed - lines changed 1, context: html, text, full: html, text
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  • src/hg/bedIntersect/tests/input/bigBlock.bed - lines changed 1, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/input/subBlocks.bed - lines changed 21, context: html, text, full: html, text
  • src/hg/bedIntersect/tests/makefile - lines changed 120, context: html, text, full: html, text
• Added subtracks to 1000 Genomes coverage-masking: unions across populations & masking types (Redmine Track #1079). Intersected the union subtracks with snp130 to make 'bad apples' tracks requested by Mary-Claire King (Redmine Track #1261). The 'bad apples' tracks need a new name and a description still, but the data are under review by MCK and colleagues.
  • src/hg/makeDb/doc/hg18.txt - lines changed 139, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 44, context: html, text, full: html, text
• Added some missing hFreeConn's and removed one dead-code hFreeConn.
  • src/hg/hgTracks/altGraphXTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text
• Updated gwasCatalog in hg18 and hg19.
  • src/hg/makeDb/doc/hg18.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text
• Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
  • src/hg/hgTracks/bamTrack.c - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.nt.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.nt.ra - lines changed 2, context: html, text, full: html, text
• Tweaked a comment to finish work on Redmine Feature #1093.
  • src/hg/hgTracks/bamTrack.c - lines changed 3, context: html, text, full: html, text