Commits · 35f181ba759e7aaba04f22ae9a4c3f6f2826c1c2 · R3 / legacy / bedtools2

Oct 29, 2013
- Fixed small memory leak in InputStreamMgr. · 35f181ba
  nkindlon authored 11 years ago
  
  35f181ba
- Fixed test for Bam vs Bgzip to allow for empty references. · b8d8856c
  nkindlon authored 11 years ago
  
  b8d8856c
Oct 28, 2013
- Added support for Bgzip from files and stdin. · fb901324
  nkindlon authored 11 years ago
  
  fb901324
Oct 15, 2013
- added fifo handling · 88ac8da9
  nkindlon authored 11 years ago
  
  88ac8da9
Oct 11, 2013
- Stopped BinTree from loading or getting hits for unmapped reads. · 8085e45a
  nkindlon authored 11 years ago
  
  8085e45a
Oct 09, 2013
- Moved short circuit for BAM unmapped reads to Record::sameChromIntersect for... · 8fe692c5
  nkindlon authored 11 years ago
  
  Moved short circuit for BAM unmapped reads to Record::sameChromIntersect for when query record isn't BAM but DB record is.
  8fe692c5
Oct 04, 2013
- added BamRecord::printUnmapped method for noHit and count functionality. · 5795975f
  nkindlon authored 11 years ago
  
  5795975f
Sep 29, 2013
- Fixed unmapped mate bug · 79daf360
  nkindlon authored 11 years ago
  
  79daf360
Sep 27, 2013
- Fixed chromId bug, removed debug metric from RecordOutputMgr · 6d3c94d1
  nkindlon authored 11 years ago
  
  6d3c94d1
Sep 26, 2013
- Added -g option and descriptor to intersect help message. · c1ce3e72
  nkindlon authored 11 years ago
  
  c1ce3e72
- Shortened output buffer, corrected Chromsweep errors with some print options... · e940859f
  nkindlon authored 11 years ago
  
  Shortened output buffer, corrected Chromsweep errors with some print options due to early termination.
  e940859f
Sep 24, 2013
- handling for unmapped Bam records · 60223993
  nkindlon authored 11 years ago
  
  60223993
- add missing include to prevent compilation error · 0581bad9
  Aaron R. Quinlan authored 11 years ago
  
  0581bad9
Sep 20, 2013
- Improved help and error msgs in Context · 8219b6d9
  nkindlon authored 11 years ago
  
  8219b6d9
Sep 19, 2013
- fixed negative coords, zero len intervals, Bed4 format error · ca4265ec
  nkindlon authored 11 years ago
  
  ca4265ec
Sep 13, 2013
- resolved chromId problem when doing Chromsweep with BAM file sorted differently than genome file. · 36fdad10
  nkindlon authored 11 years ago
  
  36fdad10
Sep 12, 2013
- -g (genomeFile) option now gives error if file is differently sorted than genome file. · 052c0638
  nkindlon authored 11 years ago
  
  052c0638
Sep 11, 2013
- Corrected intersect showHelp segfault. · 82e1f598
  nkindlon authored 11 years ago
  
  82e1f598
Sep 10, 2013
- added sandbox and regressTest · c2fb3e5c
  nkindlon authored 11 years ago
  
  c2fb3e5c
- added more utils · 05a364e4
  nkindlon authored 11 years ago
  
  05a364e4
- added other util directories · 1435a95a
  nkindlon authored 11 years ago
  
  1435a95a
- forgot intersectFile · a1b9dcff
  nkindlon authored 11 years ago
  
  a1b9dcff
- First commit for new 2.18-alpha branch. · 69d82a78
  nkindlon authored 11 years ago
  
  69d82a78
Aug 25, 2013
- [BUG] -split, -tag and BED6 output was not implemented. · ab7bbbe4
  Aaron authored 11 years ago
  
  ab7bbbe4
Aug 14, 2013
- [DOC] add docs for the -noOverlapping option in shuffle. · 79fa169d
  Aaron authored 11 years ago
  
  79fa169d
- [ENH] add -mate1 option for -bedpe output in bamtobed · eab9849e
  Aaron authored 11 years ago
  
  eab9849e
Jun 27, 2013
- ENH: shuffle intervals to non-overlapping locations. · 763e1c72
  Brent Pedersen authored 11 years ago
  
  763e1c72
Apr 30, 2013
- report which chrom can't be found in -incl · 1e182340
  Aaron authored 11 years ago
  
  1e182340
Feb 13, 2013
- add n_intersections to jaccard output · 3b468dd3
  Brent Pedersen authored 12 years ago
  
  3b468dd3
Feb 01, 2013
- Build these objects only once · 81ed020d
  John Marshall authored 12 years ago
  
  Because $(SOURCES) contains non-.cpp files, object files were being built twice, once as .o and once (somewhat by luck!) as .h.
  81ed020d
- Ignore generated source files and library · c0fa791f
  John Marshall authored 12 years ago
  
  c0fa791f
Jan 29, 2013
- [EHN] add -delim option to bedtools merge · 65e377d2
  Aaron authored 12 years ago
  
  65e377d2
Jan 09, 2013
- [ENH] support MS Windows line endings (\r\n). Output is always \n · 37c85753
  Aaron authored 12 years ago
  
  37c85753
Dec 27, 2012
- [ENH] Properly handle empty, yet existent files. Thanks to @jpaulLD and @jmarshall. · ca50f590
  Aaron authored 12 years ago
  
  ca50f590
Dec 26, 2012
- [BUG] Fix regression in reporting all overlapping features for . Thanks to @jsilter. · 2a16ea92
  Aaron authored 12 years ago
  
  2a16ea92
- [BUG] Removed unnecessary pointer deletion in tag's destructor. Cheers to @yarden and @jmarshall. · 1be59744
  Aaron authored 12 years ago
  
  1be59744
- [ENH] jaccard now works in a single pass. · bc14bfde
  Aaron authored 12 years ago
  
  bc14bfde
Dec 19, 2012
- [ENH] user controls MAX_TRIES (-maxTries) in shuffle. · 5ce8ff0e
  Aaron authored 12 years ago
  
  5ce8ff0e
Dec 17, 2012
- [BUG] typo in database length calc. · 15368736
  Aaron authored 12 years ago
  
  15368736
Dec 13, 2012
- Fixed segfault with -names option in tagBam · be157901
  Paul Ryvkin authored 12 years ago
  
  be157901