broadinstitute/picard

Fixes #886.

…ult-DSDEGP-454

DSDEGP-454 Enable the IntelDeflater by default in all invocations of Picard

…or library) (#642)


* new CLP CrosscheckFingerprints can crosscheck bams and vcfs
* added option to crosscheck by input file
* added choice of output format: Matrix or Metric File. Metric File outputs contains the LOD score and also the tumor-aware LOD scores.
* Includes tumor-aware results when results are emitted as a metric file
* new CLP ClusterCrosscheckMetrics that will take the metric output of CrosscheckFingerprints and find clusters of groups that connect with a high LOD
* tests refactored
* general purpose graph-clustering algorithm added
* removed deprecated GenotypeReader class
* add a deprecated wrapper named CrosscheckReadgroupFingerprints for backwards continuity
* crosscheck now allows missing RG tags in bam if VALIDATION_STRINGENCY is not STRICT.

* Adding the COVERED action to interval list tools: find only intervals in INPUT that have any overlap with SECOND_INPUT.
* Update htsjdk to 2.10.1

* -reved htsjdk to 2.9.1

* - fixed ambiguous constructor with null in test

The gradle task createMetricsDoclet wasn't actually doing anything. This fixes it so that it runs and creates the appropriate html.

this should help ease some development pains by allowing use of composite builds and other new gradle features

-rev htsjdk to 2.7.0
- remove usage of deprecated code
- some java8 sugar

fixes #617

let the htsjdk version to build against be specied as a system property on the command line

ex:

./gradlew test -Dhtsjdk.version=someversion

this lets picard be built against artifactory snapshots of htsjdk
picard MUST NOT be released if using an artifactory snapshot (and probably cannot be)