Commits · 1cb82b334f087d978f48cebe7a66e1e3c1f21e7c · R3 / legacy / bedtools2

Jul 24, 2012
- include html · 1cb82b33
  Aaron authored 12 years ago
  
  1cb82b33
- added docs/_build. working on plots via @daler · a79c662d
  Aaron authored 12 years ago
  
  a79c662d
Jul 21, 2012
- first cut at sphinx-based docs · 356dc38a
  Aaron authored 12 years ago
  
  356dc38a
- slightly better randomization · ebd31372
  Aaron authored 12 years ago
  
  ebd31372
- reset each bedpe · 956e384b
  Aaron authored 12 years ago
  
  956e384b
- no need for flanks to the left of chrom.start · 71f9e102
  Aaron authored 12 years ago
  
  71f9e102
Jul 20, 2012
- added shuffle logic for BEDPE · f991233c
  Aaron authored 12 years ago
  
  f991233c
Jul 18, 2012
- added -A option to subtract entire interval when any overlap · 1830530c
  Aaron authored 12 years ago
  
  1830530c
Jul 17, 2012
- Allow user to force closest interval to have different name (-N) · e10e26ff
  Aaron authored 12 years ago
  
  e10e26ff
Jul 04, 2012
- allow \# in chrom name, just not at beg. of line (header) · ebd9d50e
  Aaron authored 12 years ago
  
  ebd9d50e
- typo. · a11df444
  Aaron authored 12 years ago
  
  a11df444
- print bedpe record immediately after unpaired read. · 63e86242
  Aaron authored 12 years ago
  
  63e86242
Jun 26, 2012
- Inital screen for -split overlaps should include the full span of A_i · 52cc6b23
  Aaron authored 12 years ago
  
  52cc6b23
- allow uint32 or int32 -tags · 9c493f8a
  Aaron authored 12 years ago
  
  9c493f8a
Jun 19, 2012
- catch missing chroms for mapped BAM alignments. warn, don't out_of_range() · 9faf708c
  Aaron authored 12 years ago
  
  9faf708c
- correct missing tab in annotate's header · 1037f567
  Aaron authored 12 years ago
  
  1037f567
Jun 09, 2012
- only write to bam if bam output req. with -v · d32b9078
  Aaron authored 12 years ago
  
  d32b9078
Jun 06, 2012
- Merge pull request #22 from agordon/bugfix/bamtobed_non_existing_file · 264bb9fc
  Aaron Quinlan authored 12 years ago
  
  BamToBed: properly fail on non-existing input files.
  264bb9fc
- regression tests for -abam w/ [-c | -wao | -wo] · 345a1f21
  Aaron authored 12 years ago
  
  345a1f21
- BamToBed: properly fail on non-existing input files. · eac4aafa
  Assaf Gordon authored 12 years ago
  
  eac4aafa
- -wo -wao -c with -abam force BED output. Thanks to @agordon. · a1f44cf7
  Aaron authored 12 years ago
  
  a1f44cf7
May 23, 2012
- genome file drives BAM header order in bedtobam · 9c98518f
  Aaron authored 12 years ago
  
  9c98518f
May 21, 2012
- fix off-by-one error in calc. -d for closest · 13dd59af
  Aaron authored 12 years ago
  
  13dd59af
May 15, 2012
- prefer empty() over size() · 09eb206e
  Aaron authored 12 years ago
  
  09eb206e
- safely handle empty input · 601760a4
  Aaron authored 12 years ago
  
  601760a4
- handle unaligned BAMs with -v · 8c626811
  Aaron authored 12 years ago
  
  8c626811
Apr 26, 2012
- remove extraneous .o · acf2ec5e
  Aaron authored 12 years ago
  
  acf2ec5e
Apr 03, 2012
- fixed logic bug in bedtobam's -bed12 mode. · 0e2b20ae
  Aaron authored 13 years ago
  
  0e2b20ae
Mar 31, 2012
- Merge pull request #20 from agordon/feature/makewindows_name_fix · 74caf83d
  Aaron Quinlan authored 13 years ago
  
  WindowMaker: bugfix with using "srcwinnum" + genome
  74caf83d
Mar 30, 2012
- WindowMaker: bugfix with using "srcwinnum" + genome · e363273b
  Assaf Gordon authored 13 years ago
  
  e363273b
- Setting Release-Version v2.16.2 · 5e19e19b
  Aaron authored 13 years ago
  
  5e19e19b
- support for bedtools existing somewhere other than PATH · 65ceb1f5
  Aaron authored 13 years ago
  
  65ceb1f5
- add omitted test dirs for "make test" · 64ed292d
  Aaron authored 13 years ago
  
  64ed292d
Mar 21, 2012
- fiddle w/ Makefile · 17053b8d
  Aaron authored 13 years ago
  
  17053b8d
- twiddle Makefile · eafbbd07
  Aaron authored 13 years ago
  
  eafbbd07
- Makefile tweak · e481a421
  Aaron authored 13 years ago
  
  e481a421
Mar 13, 2012
- Setting Release-Version v2.16.1 · d6fbc6af
  Aaron authored 13 years ago
  
  d6fbc6af
- Setting Release-Version v2.16.0 · 34a94247
  Aaron authored 13 years ago
  
  34a94247
- tweaks to bamtofastq · caaf42ea
  Aaron authored 13 years ago
  
  caaf42ea
Mar 12, 2012
- HELP: groupby -full uses first ine in group · 4ba5f455
  Aaron authored 13 years ago
  
  4ba5f455