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Commits on Sep 18, 2014
Commits on Sep 15, 2014
Commits on Sep 14, 2014
  1. bgzf: massive bug correction (also in bam)

    authored
    Bgzf:
    - incorrect write endianness
    - check valid argument in bgzf.input_string
    - incorrect isize in block
    - incorrect update of current position in uncompressed buffer
    - output_char was always writing spaces
    
    Bam:
    - length of certain NULL terminated sequences
    - write of plain SAM header
    - added more tests
Commits on Sep 11, 2014
  1. bam_alt: heavy changes in API and implementation

    authored
    the BAM module now uses an special representation of alignment
    records, which is hardly parsed. The idea is to avoid unnecessary
    parsing like CIGAR, sequence or quality decoding if it's not
    necessary.
    
    Also added more tests, which check the contents of alignments.
  2. @agarwal

    travis: pin cfstream and improve pinning

    agarwal authored
    We are again using unreleased functions of cfstream, so need to pin.
    Also pin directly to git repos. We were cloning first unnecessarily.
  3. @agarwal

    Fastq: Illumina-specific support

    agarwal authored
    Parse name strings to Illumina sequence identifiers.
  4. @agarwal
  5. @agarwal

    Fastq: improve documentation

    agarwal authored
  6. @agarwal

    Fastq: remove deprecated API

    agarwal authored
    We previously implemented our new style of API, i.e. using Or_error and
    Future. Now deleted old functions and error types.
  7. @agarwal
  8. @agarwal

    stop compiling Tags and most apps

    agarwal authored
    We are making broad changes and it was difficult to do so since Tags
    depends on every module. Removing it and all the apps that depend on it
    will simplify development at this time.
    
    All affected files moved into a tmp/ directory, so we can still
    remember the code that needs to be re-incorporated.
Commits on Sep 10, 2014
  1. Sam: constructors for cigar_op

    authored
    as cigar_op is a private type, we need constructors to build them from
    BAM, which has a different encoding of CIGAR operations than SAM (so
    the parser does not help here)
    
    Also private row polymorphic types have switched from open to closed,
    to allow exhaustivity checks outside of the Sam module.
Commits on Sep 9, 2014
  1. @agarwal

    Roman_num: improve API

    agarwal authored
    Rename functions. Return Or_error and provide exception-less versions
    in Biocaml_ez. Move debugging code into new tests module. Whitespace
    and documentation improvements.
  2. @agarwal

    rename RomanNum to Roman_num

    agarwal authored
    To follow our module naming convention.
Commits on Aug 23, 2014
  1. @agarwal

    Strand: improve API

    agarwal authored
    * Make type be a private char.
    * Use new convention of being exception-less.
    * Provide constants: minus and plus.
    * of_string now accepts more strings.
    * Remove compare and equal functions.
    * minus_plus now return a char instead of a string.
  2. @agarwal

    rename module StrandName to Strand

    agarwal authored
    It’s simpler, and StrandName’s camel casing wasn’t following our module
    naming convention of using underscores.
  3. @agarwal

    speedup and improve Travis builds

    agarwal authored
    OPAM now has a binary distribution, so use that. Speedup might result
    from setting OPAMJOBS since Travis build machines have 2 cores.
    Avoiding installation of OCaml system compiler won’t help because we
    now have to install one at opam-init time instead.
    
    Also simplify pinning. No longer need to add future-dev repo due to new
    opam features.
Commits on Aug 19, 2014
  1. @agarwal

    opam: add version constraint on camlzip

    agarwal authored
    We require the `zip` findlib package, which is not provided by camlzip
    1.04 (as mentioned in #144). We could instead require `camlzip`, which
    would make us compatible with all versions of camlzip. However, it
    seems 1.05 is deprecating the `camlzip` findlib package name in favor
    of `zip` (because camlzip is defined as an alias to zip, the library
    file is zip.cma). Thus, might as well go with that.
Commits on Aug 17, 2014
  1. @agarwal

    opam: update for opam 1.2 features

    agarwal authored
    Separate out install target. Add bug-reports and license field. Add
    build constraint to ocamlfind and omake.
  2. @agarwal

    simplify opam pinning for developers

    agarwal authored
    No longer need to add special repo prior to pinning biocaml. Just do
    `opam pin -k path biocaml ~/path/to/biocaml`.
Commits on Aug 10, 2014
  1. @agarwal

    Sam: remove unused opt_field_A_re

    agarwal authored
    No longer used due to db4644a.
Commits on Aug 9, 2014
  1. @agarwal

    Merge pull request #141 from pveber/master

    agarwal authored
    Sam: a constructor for optional field
  2. Sam: constructors for optional field and optional field values

    authored
    [Sam.optional_field] is a private type and the only way to build a
    value is through the [Sam.parse_optional_field] function, which is not
    adequate when parsing BAM.
    
    Added a constructor for [optional_field] which takes
    [optional_field_value]s. This is also a private type, so
    invariant-checking constructors and parsers were added too.
Commits on Aug 6, 2014
Commits on Aug 4, 2014
  1. a preliminary version of an alternative bam parser

    authored
    comes with a test and a small (and particularly unfair) benchmark
    against the transform implementation.
Commits on Aug 3, 2014
  1. @agarwal

    delete all read_file functions

    agarwal authored
    All leaked a resource. Closes #139.
  2. @agarwal

    Sam: expose parse_header

    agarwal authored
    Factor out definition from within `read` and expose. Closes #140.
  3. @agarwal

    Sam: define empty_header

    agarwal authored
    Not really that useful, but it makes it clear that the `header` type
    includes the possibility of no header, i.e. that you never need `header
    option`.
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