Commits on Nov 23, 2015
  1. @ernfrid

    Merge pull request #12 from genome/bed_chrom

    use the chromosome from the alignments in the bed output
    ernfrid committed Nov 23, 2015
  2. @ernfrid
  3. @ernfrid

    Merge pull request #11 from gatoravi/fix_bed_output

    Fix end position calculation.
    ernfrid committed Nov 23, 2015
Commits on Nov 20, 2015
  1. @gatoravi

    Update test data.

    I verified the BED read co-ordinates by looking at the NA19240 BAM
    file with 'samtools view'. The SAM format is 1-based whereas BED
    is 0-based so there is a 1 b.p difference between the SAM read position
    and the BED start.
    gatoravi committed Nov 20, 2015
  2. @gatoravi

    Fix zero-based calculation.

    gatoravi committed Nov 20, 2015
Commits on Nov 18, 2015
  1. @gatoravi

    Fix end position calculation.

    gatoravi committed Nov 18, 2015
Commits on Oct 9, 2015
  1. @ernfrid
Commits on Jul 31, 2015
  1. @ernfrid

    Create README.md

    ernfrid committed Jul 30, 2015
  2. @ernfrid

    Add MIT License

    ernfrid committed Jul 30, 2015
Commits on Jun 17, 2015
  1. @ernfrid

    Merge pull request #2 from genome/gtest_compilation

    Tests cannot find tr1/tuple on Max OS X
    ernfrid committed Jun 16, 2015
  2. @tabbott
  3. @tabbott

    add PreDepends cmake module to build common

    the intent is to enable parallel builds without having to "make deps"
    first. this is done by hijacking externalproject_add, add_library, and
    add_executable with macros that automatically set dependencies on a
    dummy "deps"-like target.
    tabbott committed Jun 12, 2015
Commits on Jun 12, 2015
  1. @ernfrid

    Tests cannot find tr1/tuple on Max OS X

    Adding the compiler flag fixes this on 10.10.3
    with Apple LLVM version 6.1.0 (clang-602.0.53)
    ernfrid committed Jun 11, 2015
Commits on Jun 10, 2015
  1. @ernfrid

    not explicitly casting to boolean return value causes errors on newer…

    … compilers (AppleClang).
    ernfrid committed Jun 10, 2015
  2. @ernfrid
Commits on Apr 13, 2015
  1. @ernfrid
Commits on Mar 14, 2015
  1. @ernfrid
Commits on Mar 13, 2015
  1. @ernfrid
Commits on Mar 9, 2015
Commits on Mar 6, 2015
  1. remove extra newline from package description

    Travis Abbott committed Mar 6, 2015
Commits on Aug 7, 2014
  1. add package version suffix to cpack info

    Travis Abbott committed Aug 7, 2014
  2. don't append PACKAGE_VERSION_SUFFIX to FULL_VERSION

    instead, cpack files should be modified to reference
    PACKAGE_VERSION_SUFFIX directly (FULL_VERSION has other uses)
    Travis Abbott committed Aug 7, 2014
  3. don't append PACKAGE_VERSION_SUFFIX to FULL_VERSION

    instead, cpack files should be modified to reference
    PACKAGE_VERSION_SUFFIX directly (FULL_VERSION has other uses)
    Travis Abbott committed Aug 7, 2014
  4. Merge commit '5c3fe36b9fc2828a30544fc69ba4bbce2e58cb6c'

    update build-common
    Travis Abbott committed Aug 7, 2014
  5. Squashed 'build-common/' changes from 667edee..d356b1b

    d356b1b always use gtests tr1/tuple
    8e9db39 make sure tests link w/threads lib
    
    git-subtree-dir: build-common
    git-subtree-split: d356b1b
    Travis Abbott committed Aug 7, 2014
Commits on Jul 23, 2014
  1. @acoffman

    fix typo in file path

    acoffman committed Jul 23, 2014
  2. @acoffman

    update config for new gmt site

    acoffman committed Jul 23, 2014
Commits on Jul 17, 2014
  1. always use gtests tr1/tuple

    Travis Abbott committed Jul 17, 2014
Commits on Jul 7, 2014
  1. ignore supplemental alignments

    Travis Abbott committed Jul 7, 2014
Commits on Jun 30, 2014
  1. make sure tests link w/threads lib

    Travis Abbott committed Jun 30, 2014
Commits on Jun 18, 2014
  1. switch reads to shared ptrs to avoid copying

    Travis Abbott committed Jun 18, 2014
Commits on Jun 15, 2014
  1. Alignment class surgery:

    remove unused code/vars, general code cleanup
    Travis Abbott committed Jun 14, 2014
Commits on Jun 14, 2014
  1. fix CTX check in BreakDancer

    don't skip CTX reads in CTX only modes. that's just silly!
    Travis Abbott committed Jun 14, 2014