Commits · f36d6db42bde718b1f8e08acd175d55cffd77e56 · R3 / legacy / bedtools2

Apr 08, 2014
- Merge converted to PFM, first check-in · f36d6db4
  nkindlon authored 10 years ago
  
  f36d6db4
Feb 28, 2014
- forgot main Makefile update. · 8bba8822
  nkindlon authored 11 years ago
  
  8bba8822
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
- Refactored contexts for validation, added unit tests, enabled -plit for map. · b912d88c
  nkindlon authored 11 years ago
  
  b912d88c
Jan 12, 2014
- first pass at using Context and PFM for the map tool. · c87afc9f
  arq5x authored 11 years ago
  
  c87afc9f
Dec 16, 2013

Changed main Makefile to put LDFLAGS after -lbamtools. Fixes customized... · 074a146c

nkindlon authored 11 years ago

Changed main Makefile to put LDFLAGS after -lbamtools. Fixes customized Bamtools link error when Bamtools already defined in /usr/lib.

074a146c

Nov 26, 2013
- Added sample sub-program with needed changes to main, Makefiles, Context,... · b1aa9ab7
  nkindlon authored 11 years ago
  
  Added sample sub-program with needed changes to main, Makefiles, Context, FileRecordMgr, and RecordOutputMgr.
  b1aa9ab7
Sep 10, 2013
- First commit for new 2.18-alpha branch. · 69d82a78
  nkindlon authored 11 years ago
  
  69d82a78
Nov 04, 2012
- [NEW] Added new "reldist" tool to measure the distribution of relative distances between two files · 5a218193
  Aaron authored 12 years ago
  
  5a218193
Nov 02, 2012
- added new jaccard tool. see PMID: 22693437 · 425bdeaa
  Aaron authored 12 years ago
  
  425bdeaa
Jul 24, 2012
- use correct Makefile · 992c47cc
  Aaron authored 12 years ago
  
  992c47cc
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 09, 2012
- auto-version: fix missing git detection · 8284dfb0
  Assaf Gordon authored 13 years ago
  
  8284dfb0
- autoversion: fix typo in git directory name · 29c3f995
  Assaf Gordon authored 13 years ago
  
  29c3f995
- go back to gitversion · b8732891
  Aaron authored 13 years ago
  
  b8732891
- add new bamtofastq tool. · 6c5a7ead
  Aaron authored 13 years ago
  
  6c5a7ead
- Second attemp at automatic versioning system. · f6ca38cf
  Assaf Gordon authored 13 years ago
  
  Handles missing ".git" repository, and GitHub's "Download as ZIP" builds
  f6ca38cf
- s/gitversion/version/ · b283aca0
  Aaron authored 13 years ago
  
  b283aca0
- make gitversion optional · 477a1c8d
  Aaron authored 13 years ago
  
  477a1c8d
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 18, 2012
- Added expand tool. · 444d5bce
  Aaron authored 13 years ago
  
  444d5bce
Feb 17, 2012
- 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
Feb 16, 2012
- Makefile: Auto-generate version string from Git version · 48adeca0
  Assaf Gordon authored 13 years ago
  
  48adeca0
Feb 12, 2012
- 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 05, 2012
- Fix make clean to erase bamtools objects. Thanks to John Marshall. · 9f2bb68f
  Aaron authored 13 years ago
  
  9f2bb68f
- Makefile tweak · ecd4b527
  Aaron authored 13 years ago
  
  ecd4b527
Jan 31, 2012
- Added beginnings of regression testing framework. · affee5d2
  Aaron authored 13 years ago
  
  affee5d2
Jan 17, 2012
- First cut at BlockedIntervals class to cleanup spliced BAMs and BED12 · 2f6dfe9c
  Aaron authored 13 years ago
  
  2f6dfe9c
Jan 12, 2012
- Added new ops to mapBed · 51ac315b
  Aaron authored 13 years ago
  
  51ac315b
Jan 11, 2012
- store all input fields and the indices of "extra" fields. · c1176648
  Aaron authored 13 years ago
  
  c1176648
Dec 30, 2011
- Added groupby back into the bedtools package. · bcffe100
  Aaron authored 13 years ago
  
  bcffe100
- added cluster tool. both cluster and merge require sorted files for efficiency. · 761d4a58
  Aaron authored 13 years ago
  
  761d4a58
Dec 29, 2011
- Added makewindows sub-command · fbb65994
  Aaron authored 13 years ago
  
  fbb65994