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Closes #375:

  • Migrates to Hadoop-BAM 7.0.0
  • Moves from samtools/picard/tribble/variant to htsjdk 1.118

HT to @AndreSchumacher

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Rebased on master.

@fnothaft fnothaft changed the title Upgrade to Hadoop-BAM 7.0.0. [ADAM-375] Upgrade to Hadoop-BAM 7.0.0. Sep 12, 2014
@fnothaft fnothaft added this to the 0.14.0 milestone Sep 13, 2014
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Rebased.

@tdanford
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Can you rebase one more time, @fnothaft?

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Rebased!

@fnothaft
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Rererebased.

@fnothaft
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Rerererebased.

@@ -49,7 +49,7 @@
* format.
*
* This reader is based on the FastqInputFormat that's part of Hadoop-BAM,
* found at http://sourceforge.net/p/hadoop-bam/code/ci/master/tree/src/fi/tkk/ics/hadoop/bam/FastqInputFormat.java
* found at http://sourceforge.net/p/hadoop-bam/code/ci/master/tree/src/org.seqdoop.hadoop_bam/FastqInputFormat.java
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This URL returns a 404. Search-replace issue?

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Ja. Will fix...

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massie commented Sep 16, 2014

Once the URL is fixed, I'm ready to merge this. Thanks, Frank!

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Rererererebased + URL fixed.

massie added a commit that referenced this pull request Sep 16, 2014
[ADAM-375] Upgrade to Hadoop-BAM 7.0.0.
@massie massie merged commit d1d64e2 into bigdatagenomics:master Sep 16, 2014
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massie commented Sep 16, 2014

Thanks, Frank!

@fnothaft fnothaft deleted the htsjdk-migration branch September 16, 2014 22:10
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Move to htsjdk/new Hadoop-BAM
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