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Commits on Nov 30, 2011
  1. Bumped version to v0.9.18

    jts committed Nov 30, 2011
  2. Fixed configure script to properly handle bamtools include/lib paths …

    jts committed Nov 30, 2011
    …in the case where it was installed with make install
Commits on Nov 28, 2011
  1. Fixed two performance issues in sga assemble.

    jts committed Nov 28, 2011
    For very complex graphs with repetitive genomes, Myers' transitive
    reduction algorithm can take a very long time to complete.
    Since sga overlap does not output transitive edges, in the
    general use case Myers' algorithm is not needed. So it is now
    turned off by default.
    
    Second, the small repeat resolution algorithm can also take a long time
    to run. I'm attempting a fix here where I limit to run on not-too-
    complex vertices.
Commits on Nov 11, 2011
  1. In configure, specify -lbamtools in LIBS instead of LDFLAGS. This cor…

    jts committed Nov 11, 2011
    …rects the library link ordering and fixes the build in the case --as-needed is used in ld, as in newer versions of gcc.
Commits on Nov 10, 2011
Commits on Nov 8, 2011
  1. Changed sga walk to remove contained reads and lingering transitive e…

    jts committed Nov 8, 2011
    …dges when --component-walks is specified.
Commits on Oct 28, 2011
  1. Merged Albert Villela's change which allows adding a suffix to each r…

    jts committed Oct 28, 2011
    …ead ID in sga preprocess
Commits on Oct 19, 2011
  1. Set the bamtools link flag in the case that bamtools is installed in …

    jts committed Oct 19, 2011
    …a standard directory and --with-bamtools is not needed.
Commits on Oct 12, 2011
  1. v0.9.17

    jts committed Oct 12, 2011
Commits on Oct 10, 2011
  1. v0.9.16

    jts committed Oct 10, 2011
Commits on Oct 4, 2011
Commits on Oct 3, 2011
  1. v0.9.15

    jts committed Oct 3, 2011
  2. Added strict mode to scaffolder to only keep unambiguous connections …

    jts committed Oct 3, 2011
    …in the scaffold graph
Commits on Sep 28, 2011
  1. Added new filter to filterBAM to aggressively get rid of FR contamina…

    jts committed Sep 28, 2011
    …tion in a mate pair library. Added new output to the Scaffold
Commits on Sep 27, 2011
  1. Merge branch 'hapgen'

    jts committed Sep 27, 2011
    Conflicts:
    	src/SGA/correct-long.cpp
Commits on Sep 25, 2011
Commits on Sep 23, 2011
  1. hapgen: added function to MultiAlignment to construct an MA from loca…

    jts committed Sep 23, 2011
    …l alignments. Added code to hapgen to pull out read pairs.
Commits on Sep 22, 2011
  1. Merge branch 'metagenomics' into gapfill

    jts committed Sep 22, 2011
    Conflicts:
    	src/Algorithm/Makefile.am
    	src/SGA/Makefile.am
    	src/SGA/sga.cpp
Commits on Sep 21, 2011
Commits on Sep 20, 2011