Picard release 1.85
7 February 2013
- bug fix -- LittleEndianInputStream would hang in infinite loop if EOF was encountered before null terminator.
- Include tribble build/tests in main build.xml, some refactoring. Use sam version number for tribble
- Move org.broadinstitute.variant to the Picard repo
-Modified build.xml to build and package the variant classes
into a separate jar
-Made the necessary changes to run our unit tests with
Contracts for Java enabled. These now run as part of a normal
"ant test". Note that our tests are not as "chatty" as yours,
so there will be a short pause in the output while the variant
-Add the required cofoja (Contracts for Java) and Apache commons
dependencies to lib/
- Moving JEXLMap from a top level member of file VariantJEXLContext to its own class
- CollectGcBiasMetrics.java: Create command line argument (short name BS) to handle bisulfite sequenced reads. CollectGcBiasMetrics will use the bisulfite-aware countMismatches() if true.
- Adding Merge- and SplitVcfs, two utilities that merge VCF files and split them into files of only SNPs or indels. Also adding MergingIterator and a comparator for VariantContext