2.10.0
This release includes useful new features and a lot of bug fixes:
- Expanded support for
Path
to more of the api (#846, #810, #814) - There's now support for creating fasta.fai indexes (#842)
- HTSJDK tests can now be written in scala as well as java (#789)
This release includes changes to the htsjdk.tribble.Index
API. Anyone who has implemented a subclass of Index
will have to update their class See #841 and #810 for more details.
Detailed Changes:
- Revert "The existing code was throwing a NPE when using a CRAMFileReader for … (#879)" (#885)
- The existing code was throwing a NPE when using a CRAMFileReader for … (#879)
- Index.writeBasedOnFeaturePath throws instead of silently failing (#841)
- fixed a small NPE in MD5CalculatingOutputStream (#881)
- Fix ordering of assignments in FastQReader constructor. (#878)
- Adding OpenJDK8 to travis configuration (#875)
- Defensive programming around test case race condition to address #776 (#790)
- Obey the tmpDir setting in several constructors that currently ignore it (#826)
- add UNKNOWN sort order(#862)
- More informative IO error for FASTQ reader (#865)
- Add .fai index creation support (#842)
- Add fromPath to IntervalList. (#846)
- Count the number of warnings and errors during SAM file validation (#855)
- Added the ability to query the length of the line terminator to AsciiLineReader. (#843)
- removing scripts/release_picard.sh (#858)
- Adding a pre-test check that looks for java files in the test/scala d… (#857)
- Expose a couple of protected methods and replace hard coded strings with an enum. (#854)
- check for negative length in CigarElement ctor (#839)
- replace method getRefPos() into abstract class EdgingRecordAndOffset and delete constructor in AbstractRecordAndOffset (#849)
- Enabling writing and running of tests with scalatest. (#789)
- Maintain ordering of header in smartMergeHeader #847 (#848)
- Fix DateParserTest unit tests that were failing in my locale. (#832)
- Make exception message informative in SAMUtils.charToCompressedBase (#836)
- Adding getSAMString to AbstractSAMHeaderRecord (#827)
- Update javadoc for Feature (#818)
- Tribble/Tabix index path support (#810)
- Fix for issue #513: NPE in ValidateSamFile with CRAM (#735)
- fixing vararg warnings on test compilation (#809)
- support Path in Md5CalculatingOutputStream(#814)
- Fixed bug where calling IntervalList.uniqued(false) would fail if the interval names were null. (#815)
- Refactoring FastqRecord (#572)
- automatically adding @OverRide annotations (#729)
- add a coverage drop threshold to limit codecov failure spam (#803)
- fixes for issue #547