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Commits on Apr 3, 2017

• merge upstream

  ryan-williams

  committedApr 3, 2017
  b133bb5

• style nits

  ryan-williams

  committedApr 3, 2017
  6577bb0

• Merge pull request #12 from ryan-williams/paths

  ryan-williams

  committedApr 3, 2017
  013b5ca

• fix travis coveralls-disabling

  ryan-williams

  committedApr 3, 2017
  21211b1

• ContigName Factory fixes, dep cleanups

  ryan-williams

  committedApr 3, 2017
  2ce35f1

• Fix typo in header

  heuermh

  committedApr 3, 2017
  b26b851

• Modifying pom.xml files for new development after 0.22.0 release.

  heuermh

  committedApr 3, 2017
  7d9b666

• Modifying changelog.

  heuermh

  committedApr 3, 2017
  9613a4b

• [ADAM-1469] Don't filter on whether reads have mismatches during realignment

  

  fnothaft

  authored and

  heuermh

  committedApr 3, 2017
  8df3aa2

• [ADAM-1467] Skip concat call if there is only one shard.

  

  fnothaft

  authored and

  heuermh

  committedApr 3, 2017
  15aa5cd

• [ADAM-1465] Updating realigner CLI docs.

  

  fnothaft

  authored and

  heuermh

  committedApr 3, 2017
  bbcb0ef

• Merge remote-tracking branch 'b/master' into sbt

  ryan-williams

  committedApr 3, 2017
  deaa6f5

Commits on Apr 2, 2017

• style nits

  ryan-williams

  committedApr 2, 2017
  84d2187

Commits on Apr 1, 2017

• use hammerlab.paths.Path

  ryan-williams

  committedApr 1, 2017
  0f4af04

Commits on Mar 31, 2017

• Rename recalibateBaseQualities method as recalibrateBaseQualities

  

  heuermh

  authored and

  fnothaft

  committedMar 31, 2017
  a70c371

• [ADAM-1453] Add hooks to publish ADAM docs from CI flow.

  

  fnothaft

  authored and

  heuermh

  committedMar 31, 2017
  462db97

• [ADAM-1402] Fix INDEL realigner bad binary search.

  

  fnothaft

  authored and

  heuermh

  committedMar 31, 2017
  d12fdfb

Commits on Mar 30, 2017

• path+style nits

  ryan-williams

  committedMar 30, 2017
  84b42f6

Commits on Mar 29, 2017

• use Paths, upgrade utils

  ryan-williams

  committedMar 29, 2017
  e83e461

Commits on Mar 27, 2017

• Adding test for reads dropped in version 0.21.0.

  

  heuermh

  authored and

  fnothaft

  committedMar 27, 2017
  65d8c9e

• [ADAM-1455] Upgrade to Hadoop-BAM 7.8.0 and htsjdk 2.9.1

  

  fnothaft

  authored and

  heuermh

  committedMar 27, 2017
  4a74482

• Update bdg-utils dependency version to 0.2.13.

  heuermh

  committedMar 27, 2017
  86922ae

• [ADAM-1459] Don't split FASTQ when compressed.

  

  fnothaft

  authored and

  heuermh

  committedMar 27, 2017
  a9a0039

Commits on Mar 23, 2017

• upgrade hadoop_bam

  ryan-williams

  committedMar 23, 2017
  781b4cc

Commits on Mar 22, 2017

• Moving API overview from building apps doc to new source file.

  

  heuermh

  authored and

  fnothaft

  committedMar 22, 2017
  629b778

• [ADAM-1451] Make VariantContextConverter class and convert methods public.

  

  fnothaft

  authored and

  heuermh

  committedMar 22, 2017
  4c58028

Commits on Mar 21, 2017

• [ADAM-1439] Add inferSequenceDictionary ctr to FeatureRDD. (bigdatagenomics#1447)

  

  heuermh

  authored and

  fnothaft

  committedMar 21, 2017
  fd0cb6e

• [ADAM-1445] Make apply method for FragmentRDD public.

  

  fnothaft

  authored and

  heuermh

  committedMar 21, 2017
  dbf4f85

• [ADAM-1442] Fix thread pool deadlock in GenomicRDD.pipe

  

  fnothaft

  authored and

  heuermh

  committedMar 21, 2017
  95b2a86

Commits on Mar 20, 2017

• [ADAM-1358] Refactor BQSR to improve performance and legibility.

  

  fnothaft

  authored and

  heuermh

  committedMar 20, 2017
  b1fce67

• [ADAM-1164] Add parallel file merger.

  

  fnothaft

  authored and

  heuermh

  committedMar 20, 2017
  98b263f

Commits on Mar 18, 2017

• test nits, resource URL loading

  ryan-williams

  committedMar 18, 2017
  5a4764d

Commits on Mar 15, 2017

• added JavaApi for loadCoverage

  

  akmorrow13

  authored and

  heuermh

  committedMar 15, 2017
  cf39e6c

Commits on Mar 14, 2017

• Add cache argument to loadFeatures, additional Feature timers (bigdatagenomics#1427)

  

  heuermh

  authored and

  fnothaft

  committedMar 14, 2017
  9938d3c

• Add pipe API in and out formatters for Features

  

  heuermh

  authored and

  fnothaft

  committedMar 14, 2017
  b8477dc

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