File Changes for kent

v247_preview to v247_preview2 (2011-02-01 to 2011-02-08) v247

• src/hg/hgTables/asFilter.c
  • lines changed 240, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/asFilter.h
  • lines changed 81, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/asObj.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 34, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bam.c
  • lines changed 142, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 297, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 2, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/bigBed.c
  • lines changed 13, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 319, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/filterFields.c
  • lines changed 3, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 11, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/hgTables.c
  • lines changed 3, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 5, context: html, text, full: html, text
    Fixing a chromosome-table check that was glitching out selected fields output for bigBed data hub tracks.
  • lines changed 17, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 9, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 37, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/joining.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 13, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 2, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    Making big bed all field output work in hubs.
  • lines changed 4, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/hgTracks/bamTrack.c
  • lines changed 6, context: html, text, full: html, text
    Adding bam support to data hubs in hgTracks and hgc.
  • lines changed 2, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/hgc/bamClick.c
  • lines changed 8, context: html, text, full: html, text
    Adding bam support to data hubs in hgTracks and hgc.
  • lines changed 2, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Fixing typo in comment.
• src/hg/inc/bamFile.h
  • lines changed 22, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/inc/samAlignment.h
  • lines changed 72, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/lib/bamFile.c
  • lines changed 165, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/hubConnect.c
  • lines changed 48, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/samAlignment.as
  • lines changed 16, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/lib/samAlignment.c
  • lines changed 189, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/hg/lib/samAlignment.sql
  • lines changed 22, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
  • lines changed 1, context: html, text, full: html, text
    Getting Table Browser to handle BAM files. This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
• src/hg/oneShot/freen/freen.c
  • lines changed 15, context: html, text, full: html, text
    Some preliminary work putting proper bam support in table browser. Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM. This I think contains all the info.
• src/inc/errabort.h
  • lines changed 3, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/inc/linefile.h
  • lines changed 3, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/inc/net.h
  • lines changed 13, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/dystring.c
  • lines changed 3, context: html, text, full: html, text
    Making dyString expand by at least 1.5x if it needs to expand.
• src/lib/errabort.c
  • lines changed 13, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/linefile.c
  • lines changed 12, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/lib/net.c
  • lines changed 25, context: html, text, full: html, text
    Making it so that track html description is fetched for hgc and hgTrackUi. To do this had to get a way to fetch a text file from a URL without putting up any warning messages if it was not there, which ended up requiring a new warning handler.
• src/utils/bedRemoveOverlap/empty.bed
  • lines changed 1, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/one.bed
  • lines changed 1, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/test4.bed
  • lines changed 6, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/threeLast.bed
  • lines changed 3, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/twoFirst.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/twoSecond.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
• src/utils/bedRemoveOverlap/unsorted.bed
  • lines changed 2, context: html, text, full: html, text
    Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.