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Commits on Jul 6, 2016

• all tests passed

  Evegen55

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  c9f3f89

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Commits on Jul 4, 2016

• fixed concurrency

  Evegen55

  committed
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Commits on Jul 1, 2016

• threads' work analysis

  Evegen55

  committed
  c247651

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• clear

  Evegen55

  committed
  6d7efef

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• second attempt to make a concurrent, succesfull attempt with 1 child thread

  Evegen55

  committed
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• first attempt to make a concurrent, really finished

  Evegen55

  committed
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• first attempt to make a concurrent, finished

  Evegen55

  committed
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Commits on Jun 30, 2016

• first attempt to make a concurrent

  Evegen55

  committed
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• two test have been written for:

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  Evegen55

  committed
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Commits on Jun 29, 2016

• test changes

  Evegen55

  committed
  6f8a891

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Commits on Jun 23, 2016

• Improved documentation for multiple tools including

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  dekling

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• Fixes for compile failures and warnings and test breaks vs HTSJDK master.

  tfenne

  committed
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Commits on Jun 22, 2016

• Output the read count per target.

  nh13

  committed
  d9176cb

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Commits on Jun 21, 2016

• Fixing bug in GatherVcfs. (#570)

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  nh13

  authored and

  Yossi Farjoun

  committed
  27ef4ed

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• Merge pull request #540 from nh13/nh_mergevcfs_clear_options

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  tfenne

  authored
  32db128

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Commits on Jun 13, 2016

• Modify RevertSam to set the mate unmapped flag properly for single-end data.

  ktibbett

  committed
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Commits on Jun 12, 2016

• Revert "Tag reads in duplicate sets with the representative read and the duplicate set size"

  lhogstrom

  authored
  934b217

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• Optional flag added to MarkDuplicates. If true, each record that is part of a duplicate set is tagged with the representative read that is chosen by MarkDuplicates. This is accomplished with the Re…

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  lhogstrom

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  edc548e

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Commits on Jun 10, 2016

• Merge pull request #558 from DevFactory/release/maps-with-keys-that-are-enum-values-should-be-replaced-with-enumMap-fix-1

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  ktibbett

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  e04d707

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• - fixed TN/NT bug in check fingerprints. (#534)

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  Yossi Farjoun

  authored
  cf80cec

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• squid:S1640 - Maps with keys that are enum values should be replaced with

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  Mohamed Ezzat

  committed
  cda463f

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• Merge pull request #557 from DevFactory/release/performance-method-invokes-inefficient-use-valueOf()-instead-fix-1

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  akiezun

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  9a8443f

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Commits on Jun 9, 2016

• findbugs:DM_BOOLEAN_CTOR, findbugs:DM_NUMBER_CTOR - Performance - Method invokes inefficient constructor; use static valueOf instead

  

  Mohamed Ezzat

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Commits on Jun 7, 2016

• sprucing-up ScatterIntervalsByNsTest (#543)

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  Yossi Farjoun

  committed
  d5970c4

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Commits on May 26, 2016

• Bug fix for tiny edge-case in MarkDuplicates

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  Yossi Farjoun

  committed
  85823d2

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Commits on May 25, 2016

• Make EstimateLibraryComplexity ignore secondary or supplementary records. (#547)

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  nh13

  authored and

  Yossi Farjoun

  committed
  04ed147

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Commits on May 19, 2016

• squid:S1066 - Collapsible if statements should be merged (#469)

  

  Mohamed Ezzat

  authored and

  Yossi Farjoun

  committed
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Commits on May 18, 2016

• MergeVcfs should not clear options be default.

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  nh13

  committed
  1c41d23

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Commits on May 17, 2016

• - small changes to make HetSense deterministic (#538)

  

  kbergin

  authored and

  Yossi Farjoun

  committed
  2ebfdb1

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Commits on May 13, 2016

• Fix null library name problem in LibraryIdGenerator constructor (#505)

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  Zaal Lyanov

  authored and

  Yossi Farjoun

  committed
  076bdfd

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Commits on May 9, 2016

• Allow RevertSam to output by read group. Support CRAM as output format.

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  David Shiga

  committed
  dc32b07

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• Allow RevertSam to optionally output by read group. When run with OUTPUT_BY_READGROUP=true, multiple output bams will be created, each containing the reads for a single read group. Support outputti…

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  Dave Shiga

  committed
  a5fd973

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Commits on May 4, 2016

• fixed number of bases in output (missing a + sign) (#532)

  

  Yossi Farjoun

  committed
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Commits on Apr 28, 2016

• Merge pull request #525 from nh13/nh_liftover_with_missing_fields

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  tfenne

  committed
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• New option: ALLOW_MISSING_FIELDS_IN_HEADER in LiftoverVcf.

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  nh13

  committed
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