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Commits on Aug 14, 2018

• Support Picard style interval lists. Fixes igvteam#560

  jrobinso

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Commits on Jun 18, 2018

• Finished move of libs to module path

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  davideby

  committed
  bc0d6b4

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• Updating project build and layout for Java 9+

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  davideby

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• Updated deprecation annotations

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  davideby

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Commits on Apr 3, 2018

• Merge branch 'master' into gradle_build

  davideby

  committed
  9356846

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• Allow setting max data range to zero (vs 1E-45). Fixes igvteam#517

  jrobinso

  committed
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Commits on Mar 26, 2018

• Gradle build updates, fixing unit tests

  davideby

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Commits on Mar 23, 2018

• Gradle build work-in progress

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  davideby

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Commits on Dec 14, 2017

• Keep only alignments in view (don't cache).

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  jrobinso

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Commits on Nov 9, 2017

• Support for json genomes

  jrobinso

  committed
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Commits on Nov 6, 2017

• Add "ucscID" to session object.

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  jrobinso

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Commits on Oct 31, 2017

• Support PAF format. Minimal support -- ignores cigar tag if present. Fixes igvteam#478

  jrobinso

  committed
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Commits on Sep 11, 2017

• Build updates for Java 9 tests

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  davideby

  committed
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Commits on Jul 29, 2017

• Add explicity "Color by > YC Tag" menu option, visible when YC tags are present. Selected by default. Fixes igvteam#421

  jrobinso

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Commits on Jul 22, 2017

• Genome management refactoring

  jrobinso

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Commits on Jul 19, 2017

• Refactor support for downloaded fasta files

  jrobinso

  committed
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Commits on Jul 2, 2017

• Remove blat test

  jrobinso

  committed
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Commits on Jul 1, 2017

• Disable blat test

  jrobinso

  committed
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Commits on Jun 26, 2017

• Disk cache for CRAM reference sequences

  jrobinso

  committed
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Commits on Jun 24, 2017

• Enable alternative blocked compress fasta path in .genome file. We need to keep the uncompressed fasta as well for backward compatibility.

  jrobinso

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  a01b718

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• Fix unit test

  jrobinso

  committed
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• Basic support for bgzipped fasta files. Fixes igvteam#321.

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  jrobinso

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Commits on Jun 14, 2017

• Update htsjdk, ide artifacts

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  jrobinso

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  02a2a91

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• Remove unused unit test

  jrobinso

  committed
  e23474d

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• Fix bug in sequence caching for Cram files. Big performance impact. The "ReferenceSource" object is apparently recreated frequently by the htsjdk, this was not expected or accounted for.

  jrobinso

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Commits on Jun 13, 2017

• Twobit seq support - work in progress

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  jrobinso

  committed
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Commits on May 13, 2017

• Update htsjdk

  jrobinso

  committed
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Commits on Mar 30, 2017

• Minor bug fixes in bam-lite

  jrobinso

  committed
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Commits on Mar 24, 2017

• Progress on bam lite

  jrobinso

  committed
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Commits on Mar 23, 2017

• rename files to match public class names for case sensitive build systems

  jstjohn

  committed
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Commits on Mar 17, 2017

• "lite" bam reader

  jrobinso

  committed
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Commits on Mar 10, 2017

• Ad BGUnzip class (for .bgz files)

  jrobinso

  committed
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Commits on Feb 27, 2017

• unit test maintenance

  jrobinso

  committed
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• Unit test maintenance

  jrobinso

  committed
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Commits on Feb 26, 2017

• preference mgt refactoring

  jrobinso

  committed
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