disq-0.3.8

This release includes a number of updates to dependencies, including htsjdk to version 2.24.1 and Apache Spark to 3.0.2.

Complete change list:

2abfb12 Update htsjdk dependency version to 2.24.1.
50778bd Update htsjdk dependency version to 2.24.0.
c8e1403 Update Spark dependency version to 3.0.2. (#151)

disq-0.3.7

This release includes a number of updates to dependencies, including htsjdk to version 2.23.0.

Complete change list:

98cbd8a Update Spark dependency version to 2.4.6. (#140)
4c44399 Updating to spark 3.0.1 and hadoop 3.2.1 (#141)
fb9fca1 Bump junit from 4.12 to 4.13.1
d50a385 [DISQ-148] Update htsjdk dependency version to 2.23.0 (#147)

disq-0.3.6

This release includes a bug fix for split guessing certain files with supplementary alignments and a number of updates to dependencies.

Complete change list:

808ffa9 Update for htsjdk CRAM changes. (#131)
f6f1c8d equal treatment for supplementary alignments (#137)
4fe9ba2 Bump slf4j dependency version to 1.7.30.
757d1a3 Fixing RealWorldFilesIT (#132) (#136)
ea023f1 Update Maven plugin dependency versions.
09f712a Bump Spark dependency version to 2.4.5.
24b88dc Bump htsjdk dependency version to 2.21.1.

disq-0.3.5

This release fixes a major bug which caused the SBI index to effectively be ignored even when it was specified.

f564999 Cleanup of unnecessary variable.
3aefc06 Use results from SBI index instead of ignoring them (#124) #123
25478c0 Bump Spark dependency version to 2.4.4. (#122)

disq-0.3.4

This is a minor release which primarily includes internal code cleanup.

Complete Change List:

22c5c92 Remove index merging code from src/htsjdk #68 (#121)
202e1f0 Fix calls to deprecated htsjdk APIs (#117)
65cfd22 add tests for SAM files that corrupt with adam + htsjdk 0.20.x (#120)
8dd2362 Warn on unrecognized options (fixes #25) (#118)
8cfd528 Drop oraclejdk8 on travis since it is no longer supported, and we already have openjdk8 to test Java 8 (#119)

disq-0.3.3

This release updates disq to be compatible with changes in htsjdk 2.20.0.

Complete change list:
7370ba6 Changes required to work with htsjdk 2.20.0 (#107)
9529873 Update release instructions following Louis' experience for 0.3.2 (#115)
7d6d373 Adding .idea directory to gitignore (#114)

disq-0.3.2

This is a minor release which fixes several bugs ( #108, #109, #110 ).

As of this release we now test Disq on Java 11. Java 11 support should be considered beta since spark doesn't officially support Java 11 yet.

Complete change list:
11eb512 Don't merge empty part files. Fixes #110 (#111)
4bb4334 Test on Java 11 (#106)
03339e2 BAI merge for hg38 fails with OOM (#109)
948ed61 Cannot merge tabix files with different sequence names (#108)
52649fd Parameterize Scala version (#94)
8e45fc3 Reduce warning to info on unsupported concat operation. (#104)