Commits · bb393ba8a0ee98ce486f1f6654eaa14f3b633367 · R3 / legacy / bedtools2

Feb 28, 2012
- Merge pull request #18 from agordon/feature/makefile_debug · bb393ba8
  Aaron Quinlan authored 13 years ago
  
  Makefile: add DEBUG compiler option.
  bb393ba8
- correct -abam/-wb/-bed warning · 70eeaf79
  Aaron authored 13 years ago
  
  70eeaf79
Feb 24, 2012

Makefile: extract BamTools' API creating to a separate target. · 84c19503

Assaf Gordon authored 13 years ago

Ensures the BamTools' API files are created first (before any compilation occurs).
This allows parallel builds with "make -j 4".

84c19503

Makefile: extract the sub-dir make into targets. · 915746cb

Assaf Gordon authored 13 years ago

Allows parallel make with "-j N" .
Recommended in "Managing Projects with GNU Make", chapter 6, page 109.

915746cb

Feb 23, 2012
- Makefile: add DEBUG compiler option. · 3db23b18
  Assaf Gordon authored 13 years ago
  
  To build a debug version, run "make DEBUG=1"
  3db23b18
Feb 22, 2012
- change -leftJoin to -loj. Improve help for intersect · 5e06d44f
  Aaron authored 13 years ago
  
  5e06d44f
- add -leftjoin option to bedtools intersect · 58501fa6
  Aaron authored 13 years ago
  
  58501fa6
- expand now supports - for stdin · f3d2e583
  Aaron authored 13 years ago
  
  f3d2e583
- groupby now supports - for stdin · 6ce12cfc
  Aaron authored 13 years ago
  
  6ce12cfc
Feb 19, 2012
- make stand-alone tool for expand. · 0fd0d47b
  Aaron authored 13 years ago
  
  0fd0d47b
- minor comments · 75217ab2
  Aaron authored 13 years ago
  
  75217ab2
Feb 18, 2012
- typo · 15a93965
  Aaron authored 13 years ago
  
  15a93965
- added tests for bedtools expand · 8ca6ecbe
  Aaron authored 13 years ago
  
  8ca6ecbe
- Added expand tool. · 444d5bce
  Aaron authored 13 years ago
  
  444d5bce
Feb 17, 2012
- Merge pull request #17 from agordon/feature/minimal_version_recompile · 64190f57
  Aaron Quinlan authored 13 years ago
  
  Restructure auto-git-version
  64190f57
- Restructure auto-git-version · 0efe49ed
  Assaf Gordon authored 13 years ago
  
  Compile just one object (version.o) when the git version is changed.
  0efe49ed
- re-add clean to gitversion make. Thanks to @agordon for the insight. · e152391e
  Aaron authored 13 years ago
  
  e152391e
- tweak to Makefile · 048c1d24
  Aaron authored 13 years ago
  
  048c1d24
- Improved error message for bamtobed. · b91aabd9
  Aaron authored 13 years ago
  
  b91aabd9
- Merge pull request #16 from agordon/feature/auto_git_version · 891bd9f8
  Aaron Quinlan authored 13 years ago
  
  Makefile: Auto-generate version string from Git version
  891bd9f8
Feb 16, 2012
- Makefile: Auto-generate version string from Git version · 48adeca0
  Assaf Gordon authored 13 years ago
  
  48adeca0
- added tests for cluster · f6b0439e
  Aaron authored 13 years ago
  
  f6b0439e
Feb 15, 2012
- Fixed bug preventing proper clustering. max(end) was not being updated. · ade40fc1
  Aaron authored 13 years ago
  
  ade40fc1
Feb 14, 2012
- New tests for slop and flank. Fixed chrom end bug in flank. · fbdd520f
  Aaron authored 13 years ago
  
  fbdd520f
- tweaks to help menus · 2f55ceda
  Aaron authored 13 years ago
  
  2f55ceda
Feb 13, 2012
- added new tests for merge · f1cbce92
  Aaron authored 13 years ago
  
  f1cbce92
Feb 12, 2012
- fixed bug in merge when using -n and -nms. Cleaned up logic and use VectorOps · 74cb840e
  Aaron authored 13 years ago
  
  74cb840e
- remove additional strand from intersect -bed -abam · 4151c4d2
  Aaron authored 13 years ago
  
  4151c4d2
- correct bt random's help · 2483b5d5
  Aaron authored 13 years ago
  
  2483b5d5
- new tool: bedtools random · a3c9136d
  Aaron authored 13 years ago
  
  a3c9136d
Feb 11, 2012
- Allow input files to have consecutive tabs (i.e., empty fields) · 0e3768eb
  Aaron authored 13 years ago
  
  0e3768eb
Feb 08, 2012
- speedup merge -s a bit · cb4efc54
  Aaron authored 13 years ago
  
  cb4efc54
- added multiple new tests · 95fec543
  Aaron authored 13 years ago
  
  95fec543
- choose null for mapBed · 437a9c80
  Aaron authored 13 years ago
  
  437a9c80
- fix bed12tobed6 block num for - strand. · 7826cc4c
  Aaron authored 13 years ago
  
  7826cc4c
Feb 07, 2012
- Makefile tweak; Need newline in BlockedIntervals.h · 6a9cf0bb
  Aaron authored 13 years ago
  
  6a9cf0bb
- add limits.h to VectorOps for INT_MAX · a99aa971
  Aaron authored 13 years ago
  
  a99aa971
Feb 05, 2012
- typo · dc623f6a
  Aaron authored 13 years ago
  
  dc623f6a
- added preliminary tests for map · 3b0613c8
  Aaron authored 13 years ago
  
  3b0613c8
- fixed VectorOps mode and antimode · e620be4c
  Aaron authored 13 years ago
  
  e620be4c