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Commits on Aug 24, 2016
  1. opam: fixed compilation instructions

    due to a possible bug in solvuu-build (solvuu/solvuu-build#31), the
    former instructions (`make byte ; make native`) fail at compiling
    `cmxs`, while a direct `make` invocation seems to work.
    committed Aug 24, 2016
Commits on Jul 26, 2016
Commits on Jul 15, 2016
  1. updates wrt latest solvuu-build

    agarwal committed Jul 15, 2016
Commits on Apr 28, 2016
  1. Merge pull request #159 from ihodes/fix-vcf-parser

    Fix the VCF parser
    committed Apr 28, 2016
  2. Fix the VCF parser

    Two issues fixed
    
    1. split on \t now instead of space, cf. the spec
    2. QUAL can be . (None)
    
    Changed the tests to reflect this & modified a row to serve as a
    regression test for the QUAL issue.
    ihodes committed Apr 27, 2016
Commits on Apr 27, 2016
  1. Merge pull request #156 from ihodes/patch-1

    Remove typo from module comment
    committed Apr 27, 2016
Commits on Apr 26, 2016
  1. Remove typo from module comment

    ihodes committed Apr 26, 2016
Commits on Mar 6, 2016
  1. A benchmark for line splitting

    committed Mar 6, 2016
Commits on Feb 24, 2016
  1. Merge branch 'solvuu_build'

    This commit replaces omake by the solvuu_build ocamlbuild plugin for
    compilation. This build system features:
    - declarative description of the libraries, apps and their
      dependencies
    - compilation unit discovery (no need to list modules in each library)
    - conditional compilation (a library/app can be omitted if it depends
      on an ocamlfind package that is not installed, or a library that is
      omitted)
    - C code compilation (automated discovery of compilation units)
    - generation of project files (META, .ocamlinit, .merlin)
    - a Utop-friendly ocamlfind installation of sublibraries
    committed Feb 24, 2016
Commits on Feb 23, 2016
  1. .gitignore: update wrt to new build system

    Stop ignoring OMake files, and start ignoring files generated by our
    new ocamlbuild based build.
    agarwal committed Feb 23, 2016
  2. Solvuu_build-based compilation

    committed Feb 23, 2016
Commits on Feb 17, 2016
  1. opam: fix deps

    lwt and async are not optional
    flow is not used at all anymore
    core can't be used past version 111.13.00
    ounit is required
    committed Feb 17, 2016
  2. opam: added dev-repo field

    committed Feb 17, 2016
  3. Release of v0.4.0

    committed Feb 17, 2016
  4. removed version constraint on future

    not needed now that future's been released
    committed Feb 17, 2016
  5. updated Changes

    committed Feb 17, 2016
Commits on Feb 10, 2016
  1. benchmark: added SAM count subapp

    It can be used to compare the current SAM parser with the previous
    (transform-based) implementation.
    committed Feb 10, 2016
  2. Bam: fixed bug on quality parsing

    I wrongly assumed that quality was encoded in Phredscore + 33 while it
    is simply Phredscore (as clearly stated by spec p13 in the table)
    committed Feb 10, 2016
  3. .ocamlinit: fixed library names

    committed Feb 10, 2016
  4. benchmark/Bamcount: minor fixes

    committed Feb 10, 2016
Commits on Jan 29, 2016
  1. drop -unix suffix from lib names

    agarwal committed Jan 29, 2016
Commits on Jan 16, 2016
Commits on Nov 9, 2015
  1. bgzf: fixed decompression + added 2 tests

    in my first attempt at using zlib for bgzf decompression, I would use
    a single zlib stream to decompress all bgzf items. I don't understand
    why it worked so far, but I found new BAM files where this
    systematically fails with a wrong CRC32. I fell back to using a new
    zlib stream for each item (similar to what I was doing for output),
    the code is simpler to follow and does work on the new test files.
    committed Nov 9, 2015
Commits on Oct 19, 2015
  1. unix/{Sam, Bam}: implement correct encoding of integers in optional v…

    …alues
    
    Following our request [0], the spec for SAM and BAM formats was
    updated. This commit implements the corresponding change.
    
    Closes #145.
    
    [0] samtools/hts-specs#36
    committed Oct 19, 2015
Commits on Oct 18, 2015
  1. unix/Sam: fixed warnings

    - removed label from binary bind operator
    - made error message more explicit
    committed Oct 18, 2015
  2. Merge branch 'bam-module'

    Bam_alt module becomes the default implementation for BAM related functionalities
    committed Oct 18, 2015
  3. Bam_alt becomes the new default implementation for BAM-related functi…

    …onalities
    
    - Bam_alt -> Bam
    - Bam -> Transform_bam in benchmark (I think it's useful to keep
      performance comparison for a little while)
    - Sam_deprecated -> Transform_sam in benchmark
    - deprecated tests commented out in test/Sam
    committed Oct 18, 2015
  4. unix/Bam_alt: commenting

    committed Oct 18, 2015