samtools/htsjdk

Broke out the static VCF suffix variables so that they can be used separately.

…sed separately.

Updated javadocs for query method

* Deprecate SAMTools.java because it is confusing and of very limited use, as well as being untested and unmaintained.

* Full coverage for CigarElement
* Full coverage for CigarOperator
* Increase Cigar coverage and test explicitly some methods

… provider. (#940)

* added a new method which allows the logger to be redirected to a different stream other than stdout.  This allows logging to be redirected to a file or other destination.

Some tests were being skipped because they weren't marked as HtsjdkTest

…ckCompressedOutputStream. (#901)

* seek() checks for negative position argument value
* tests

Fixed flipped sign when comparing read paired flags

Fix SAMRecord.getReadLength() so it does not throw an exception if null bases

* the Broad artifactory moved from a self hosted repository at artifactory.broadinstitute.org
to a web based artifactory at broadinstitute.jfrog.io/broadinstitute/
this was causing our snapshot uploads to fail
* updating our snapshot repository to point to the new link
* the old artifactory has a redirect in place to the new artifactory so
artifacts relying on the old url should still resolve.  For unknown
reasons this redirect doesn't work with gradle uploads, probably a
gradle bug.

* Fixing-up SamUtils:
- adding more information to some exceptions
- fixing java-doc
- java8 <>
- if/else alignment & braces
- removed use of deprecated SAMRecordUtils class
- @Deprecated all methods and members of SAMRecordUtils
- fixed javadoc @deprecated across the board.

…ll bases

…#890)

* adding overloads of BlockCompressedInputStream.checkTerminator to support java.nio.Path and SeekableByteChannel
* adding additional tests to BlockCompressedTerminatorTest

* Adding an overlaps function to IntervalList.

Finds all intervals in the first list that overlap any interval in the
second list.

…der for … (#879)" (#885)

This reverts commit 9bef3fc.

#879)

* The existing code was throwing a NPE when using a CRAMFileReader for InputResource.Type.PATH

* Converted multiple if statements to a switch statement

* **Breaking Change**  This is an API change.  Code relying on the old behavior will have to be updated.  We believe this should have minimal impact and most clients using Index will not have to make any changes.  Anyone with their own implementation of Index should update to match the new behavior.

* Changing behavior of Index.writeBasedOnFeaturePath() to throw instead of silently failing when it was unable to write an index.

Adding OpenJDK8 to travis configuration