Commits for kent
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v247_preview to v247_preview2 (2011-02-01 to 2011-02-08) v247
- Adding input to bedRemoveOverlap test cases. Forgot and just had expected output committed.
- src/utils/bedRemoveOverlap/empty.bed - lines changed 1, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/one.bed - lines changed 1, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/test4.bed - lines changed 6, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/threeLast.bed - lines changed 3, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/twoFirst.bed - lines changed 2, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/twoSecond.bed - lines changed 2, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/unsorted.bed - lines changed 2, context: html, text, full: html, text
- Making dyString expand by at least 1.5x if it needs to expand.
- Fixing typo in comment.
- 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/hubConnect.c - lines changed 48, context: html, text, full: html, text
- Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
- Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
- Making big bed all field output work in hubs.
- src/hg/hgTables/asObj.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/bedList.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/bigBed.c - lines changed 13, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTables/hgTables.h - lines changed 4, context: html, text, full: html, text
- src/hg/hgTables/joining.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTables/schema.c - lines changed 1, context: html, text, full: html, text
- Fixing a chromosome-table check that was glitching out selected fields output for bigBed data hub tracks.
- src/hg/hgTables/hgTables.c - lines changed 5, context: html, text, full: html, text
- Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
- Adding bam support to data hubs in hgTracks and hgc.
- src/hg/hgTracks/bamTrack.c - lines changed 6, 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/hgTables/bam.c - lines changed 142, context: html, text, full: html, text
- src/hg/hgTables/hgTables.h - lines changed 9, context: html, text, full: html, text
- src/hg/hgTables/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/bamTrack.c - lines changed 2, context: html, text, full: html, text
- src/hg/inc/samAlignment.h - lines changed 72, context: html, text, full: html, text
- src/hg/lib/samAlignment.as - lines changed 16, context: html, text, full: html, text
- src/hg/lib/samAlignment.c - lines changed 189, context: html, text, full: html, text
- src/hg/lib/samAlignment.sql - lines changed 22, context: html, text, full: html, text
- src/hg/oneShot/freen/freen.c - lines changed 15, context: html, text, full: html, text
- Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
- 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.c - lines changed 240, context: html, text, full: html, text
- src/hg/hgTables/asFilter.h - lines changed 81, context: html, text, full: html, text
- src/hg/hgTables/asObj.c - lines changed 34, context: html, text, full: html, text
- src/hg/hgTables/bam.c - lines changed 297, context: html, text, full: html, text
- src/hg/hgTables/bedList.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/bigBed.c - lines changed 319, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 11, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 17, context: html, text, full: html, text
- src/hg/hgTables/hgTables.h - lines changed 37, context: html, text, full: html, text
- src/hg/hgTables/joining.c - lines changed 13, context: html, text, full: html, text
- src/hg/hgTables/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/schema.c - lines changed 4, context: html, text, full: html, text
- src/hg/inc/samAlignment.h - lines changed 1, context: html, text, full: html, text
- src/hg/lib/samAlignment.as - lines changed 1, context: html, text, full: html, text
- src/hg/lib/samAlignment.sql - lines changed 1, context: html, text, full: html, text
- Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
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