Build GATK with a locally built htsjdk or Hadoop BAM

#To build GATK with a locally built htsjdk:

1. Run 'gradle install' on your local htsjdk build. This installs the htsjdk artifact in the local maven repository.

2. In your GATK directory, modify build.gradle by adding 'mavenLocal()' to the top of the list of repository declarations used for the build (make sure to add it to the correct block - there are two sets of repository declarations - one used for the buildscript itself and one used to build the target - you want to edit the latter one).

3. Clean and build GATK. To run with IntelliJ, you'll need to re-import your gradle dependencies.

#To build GATK with a locally built Hadoop-BAM:

1. In you Hadoop-BAM directory, run 'mvn install'. This installs Hadoop-BAM to your local mvn repository.

2. In your GATK directory, modify build.gradle by adding 'mavenLocal()' to the top of the list of repository declarations used for the build (make sure to add it to the correct block - there are two sets of repository declarations - one used for the buildscript itself and one used to build the target - you want to edit the latter one).

3. Clean and build GATK. To run with IntelliJ, you'll need to re-import your gradle dependencies.

NOTE: The version of htsjdk that is used by Hadoop-BAM when running GATK is the htsjdk jar provided by GATK. This means that the you need to use a version of Hadoop-BAM that is compatible with that version of htsjdk.