/snp-pipeline

Permalink
Switch branches/tags
Nothing to show
Commits on Jun 9, 2017
  1. @stevendavis

    Fix samtools sort compatibility with samtools 0.1.19.

    stevendavis committed Jun 9, 2017
    c8a0b67
Commits on Jun 6, 2017
  1. @stevendavis

    Disable syntax highlighting in the command reference - in conf.py.

    stevendavis committed Jun 6, 2017
    50b773d
  2. @stevendavis

    Revert "Disable syntax highlighting in the command reference." 

    This reverts commit af90d65.
    stevendavis committed Jun 6, 2017
    f0d9662
Commits on Jun 5, 2017
  1. @stevendavis

    Disable syntax highlighting in the command reference.

    stevendavis committed Jun 5, 2017
    af90d65
  2. @stevendavis

    Fix collect metrics failure when the fastq sequence id line is missin… 

    …g the machine or flowcell.

Conflicts:
	HISTORY.rst
    stevendavis committed Jun 2, 2017
    6ad1a5f
Commits on May 15, 2017
  1. @stevendavis

    Add links to 0.7 and 0.8 docs. Remove broken pypi download badge.

    stevendavis committed May 15, 2017
    9b33603
Commits on May 9, 2017
  1. @stevendavis

    Remove sphinx.ext.pngmath and sphinx.ext.mathjax.

    stevendavis committed May 9, 2017
    7e2066c
  2. @stevendavis

    Version and history changes for release 0.8.0.

    stevendavis committed May 9, 2017
    fb6160b
  3. @stevendavis

    Feed the TMPDIR or TMP_DIR environment variable to Picard TMP_DIR com… 

    …mand line option.
    stevendavis committed May 9, 2017
    9805512
Commits on May 8, 2017
  1. @stevendavis

    Handle broken fastq symlinks.

    stevendavis committed May 8, 2017
    b529f94
Commits on May 5, 2017
  1. @stevendavis

    Bump the release number to 0.8.0 and update history.

    stevendavis committed May 5, 2017
    c95c32b
Commits on May 4, 2017
  1. @stevendavis

    Rename regression tests to match new command names.

    stevendavis committed May 4, 2017
    a2b5039
Commits on May 2, 2017
  1. @stevendavis

    Change old script names to new subcommand names in documentation and … 

    …tests.
    stevendavis committed May 2, 2017
    989ad48
Commits on May 1, 2017
  1. @stevendavis

    Handle missing subcommand properly in Python3.

    stevendavis committed May 1, 2017
    58ceb7b
  2. @stevendavis

    Modify tox config to use old version of Biopython with python2.6.

    stevendavis committed May 1, 2017
    f5333db
  3. @stevendavis

    Repackage create_snp_reference_seq.py as cfsan_snp_pipeline snp_refer… 

    …ence.
    stevendavis committed May 1, 2017
    60b3e19
  4. @stevendavis

    Repackage calculate_snp_distances.py as cfsan_snp_pipeline distance.

    stevendavis committed May 1, 2017
    76006a3
Commits on Apr 28, 2017
  1. @stevendavis

    Repackage create_snp_matrix.py as cfsan_snp_pipeline snp_matrix.

    stevendavis committed Apr 28, 2017
    9d47476
  2. @stevendavis

    Repackage call_consensus.py as cfsan_snp_pipeline call_consensus.

    stevendavis committed Apr 28, 2017
    57c943c
Commits on Apr 27, 2017
  1. @stevendavis

    Repackage create_snp_list.py as cfsan_snp_pipeline merge_sites.

    stevendavis committed Apr 27, 2017
    3f408d8
  2. @stevendavis

    Repackage snp_filter.py as cfsan_snp_pipeline filter_regions.

    stevendavis committed Apr 27, 2017
    627d2d6
Commits on Apr 24, 2017
  1. @stevendavis

    Some Flake8 compliance cleanup.

    stevendavis committed Apr 24, 2017
    e068484
  2. @stevendavis

    Repackage copy_snppipeline_data.py as cfsan_snp_pipeline data.

    stevendavis committed Apr 24, 2017
    c8e3bfa
Commits on Apr 21, 2017
  1. @stevendavis

    Adjust Picard JVM max memory.

    stevendavis committed Apr 21, 2017
    19ffe42
  2. @stevendavis

    Repackage collectSampleMetrics.sh as cfsan_snp_pipeline collect_metrics.

    stevendavis committed Apr 21, 2017
    8d4e908
Commits on Apr 11, 2017
  1. @stevendavis

    Repackage prepSamples.sh as cfsan_snp_pipeline call_sites.

    stevendavis committed Apr 11, 2017
    57f90e6
Commits on Apr 10, 2017
  1. @stevendavis

    Refactor the code to get sample id from from a file path or dir path … 

    …-- move to utils.
    stevendavis committed Apr 10, 2017
    0fd8fb6
Commits on Apr 7, 2017
  1. @stevendavis

    The included Listeria data set is from a LM outbreak in stone fruit, … 

    …not cheese.
    stevendavis committed Apr 7, 2017
    8b5d420
  2. @stevendavis

    Fix documentation around the new duplicate reads metric.

    stevendavis committed Apr 7, 2017
    0566aae
  3. @stevendavis

    Change the composition of the included Salmonella Agona data set.

    stevendavis committed Apr 7, 2017
    d6bf97e
Commits on Apr 6, 2017
  1. @stevendavis

    Update docs. Recommend fastq-dump --origfmt option.

    stevendavis committed Apr 6, 2017
    c56eaa9
Commits on Apr 5, 2017
  1. @stevendavis

    Make Picard MarkDuplicates less verbose by default.

    stevendavis committed Apr 5, 2017
    dbe678e
  2. @stevendavis

    Add another documentation link to better explain MarkDuplicates behav… 

    …ior.
    stevendavis committed Apr 5, 2017
    a195773
Commits on Apr 4, 2017
  1. @stevendavis

    Repackage combineSampleMetrics.sh as cfsan_snp_pipeline combine_metrics.

    stevendavis committed Apr 4, 2017
    3153ac5
Commits on Mar 31, 2017
  1. @stevendavis

    Repackage prepReference.sh as cfsan_snp_pipeline index_ref.

    stevendavis committed Mar 31, 2017
    9d8c8d4