Commits · d6544e0e9dceab78257bc547f5dd57c6344dfb2c · R3 / legacy / bedtools2

Nov 25, 2014
- change fisher to use numbers of intervals rather than bases of overlap · d6544e0e
  Brent Pedersen authored 10 years ago
  
  d6544e0e
Oct 27, 2014

fix bamToFastq skipping reads after unpaired reads · 41f96cf0

Ryan Williams authored 10 years ago

It was correctly identifying reads whose “paired” flag was set, but then
it was incorrectly skipping over the read-pair that follows such an
incorrect read.

Also added a test for this behavior.

41f96cf0

Sep 18, 2014
- Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file. · 7434d8a3
  nkindlon authored 10 years ago
  
  7434d8a3
Aug 15, 2014
- Changes for multi-DB intersection. · 56761cd4
  nkindlon authored 10 years ago
  
  56761cd4
Jul 24, 2014
- make sure it doesn't accumulate · b22d89e6
  Brent Pedersen authored 10 years ago
  
  b22d89e6
- fix slop with -pct · ecb4afaa
  Brent Pedersen authored 10 years ago
  
  ecb4afaa
Jul 07, 2014
- Corrected errors caused during merge-conflict resolution · 57ed945c
  nkindlon authored 10 years ago
  
  57ed945c
Jul 04, 2014
- Check stderr is empty, not stdout (fixes test for #46) · b84b1823
  John Marshall authored 11 years ago
  
  b84b1823
Jul 02, 2014
- Multiple DB intersect support with unit tests and updated help messages. · 509cc91d
  nkindlon authored 10 years ago
  
  509cc91d
May 29, 2014
- Added new -iobuf option and unit tests. · ccd125c1
  nkindlon authored 10 years ago
  
  ccd125c1
May 23, 2014
- Fixed bug for files with no newlines. · d8c62016
  nkindlon authored 10 years ago
  
  d8c62016
- fix for slop bug in issue \#82 · 4a5fc54a
  arq5x authored 10 years ago
  
  4a5fc54a
May 22, 2014
- correct intersect unit test - was pointing to test binary · 69eb4eaa
  arq5x authored 10 years ago
  
  69eb4eaa
- More unit tests for column ops on BAM · bc90a1a0
  nkindlon authored 10 years ago
  
  bc90a1a0
May 17, 2014
- Changes fetch columns by number from BAM files. · 952140cc
  nkindlon authored 10 years ago
  
  952140cc
May 08, 2014
- Stripped whitespace and DOS endLine chars in parsing. · 2ae5c07a
  nkindlon authored 10 years ago
  
  2ae5c07a
May 06, 2014
- Updated map's unit test for allowance of numeric ops on non-num cols · 47a801b9
  nkindlon authored 10 years ago
  
  47a801b9
- Allowed numeric ops for non-numeric columns · 9ee6bac8
  nkindlon authored 10 years ago
  
  9ee6bac8
Apr 30, 2014
- Added unit test to merge to confirm precision · be32e1c1
  nkindlon authored 10 years ago
  
  be32e1c1
- Added stranded info to jaccard and merge help, fixed stranded jaccard bug · 39fffc97
  nkindlon authored 10 years ago
  
  39fffc97
Apr 25, 2014
- Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug,... · e2be0789
  nkindlon authored 10 years ago
  
  Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.
  e2be0789
Apr 24, 2014
- Made Merge only print Bed3 output for BAM, added unit test · bbda1f41
  nkindlon authored 10 years ago
  
  bbda1f41
- merge bug fixes and unit tests · b740bbf4
  nkindlon authored 10 years ago
  
  b740bbf4
Apr 17, 2014
- cleanup unit tests. · 17ec9aa9
  arq5x authored 10 years ago
  
  17ec9aa9
- Final unit tests for merge, including stranded merge bug fixes. · 1b866b6e
  nkindlon authored 10 years ago
  
  1b866b6e
Apr 16, 2014
- Unit tests and bug fixes for merge release · 5eb3b68c
  nkindlon authored 10 years ago
  
  5eb3b68c
Apr 15, 2014
- Handling empty files with headers · fe5ea0ed
  nkindlon authored 10 years ago
  
  fe5ea0ed
Apr 09, 2014
- [TST] run shuffle tests. · bcbd75b7
  arq5x authored 10 years ago
  
  bcbd75b7
- [ENH] all shuffle with -incl to follow data distribution · 4642a149
  arq5x authored 10 years ago
  
  4642a149
Apr 08, 2014
- Merge converted to PFM, first check-in · f36d6db4
  nkindlon authored 10 years ago
  
  f36d6db4
Apr 05, 2014
- fix most filetype issues. intersect still raises error with empty files. · ed71c8e0
  arq5x authored 10 years ago
  
  ed71c8e0
Mar 21, 2014
- Access data via a DATA variable, allowing to override the location. · b9c717e3
  Charles Plessy authored 11 years ago
  
  b9c717e3
- Call bedtools via the BT variable, allowing to override the location. · c1fb7ab9
  Charles Plessy authored 11 years ago
  
  c1fb7ab9
Mar 18, 2014
- Fixed slop bug when slop factor exceeds MAX signed int. · 80820201
  nkindlon authored 11 years ago
  
  80820201
Mar 04, 2014
- Fixed intersect bug so that bed query with Bam DB correctly gives bed output. Added unit test. · 95098092
  nkindlon authored 11 years ago
  
  95098092
Feb 28, 2014
- Refactored KeyListOps, Context, mapFile for KeyListOps re-usability by other tools. · 2268ee4f
  nkindlon authored 11 years ago
  
  2268ee4f
Feb 19, 2014
- Created new KeyListOps class to replace vectorOps. Converted map tool to this. · 77c1bdad
  nkindlon authored 11 years ago
  
  77c1bdad
Feb 06, 2014
- Added unit test to intersect for gff files. · bf296c8c
  nkindlon authored 11 years ago
  
  bf296c8c
- Fixed a cut/paste error in unit test comment. · d92fdfdb
  nkindlon authored 11 years ago
  
  d92fdfdb
- Refactored contexts for validation, added unit tests, enabled -plit for map. · b912d88c
  nkindlon authored 11 years ago
  
  b912d88c