Compute 5' position properly regardless of sign of inferred insert size.
RRBS QC Metrics
Add two new PrimaryAlignmentStrategies BestEndMapq and MostDistant
Revert previous change to getPairOrientation.
Improve unit tests.
Release 1.87
Switch to svn+ssh url
Better message when SortingCollection fills up TMP_DIR.
Change URL printed on error to point to new Getting Help section on project web.
Metrics updates
New program IlluminaBasecallsToFastq, which will generate either multiple sets of FASTQs demultiplexed by barcode, or single set of FASTQs for all barcodes in input.
 IlluminaBasecallsToSam refactored to support reuse of multithreading implementation in IlluminaBasecallsToFastq.
Fix incorrectly named DataProvider.
Adjust maxRecordsInRam passed to ClusterConverter so that command-line option retains approximately the same behavior as before.
ignore intellij atlassian plug-in config file
Fix build breakage due to overzealous automatic refactoring.
Increase Xmx for running test suite -- org.broad.tribble.readers.ReaderTest.testMassiveLines got an OOM
Fix long-standing bug in SamLocusIterator in which every other locus was being skipped when emitUncoveredLoci==true and not using an interval list file.
Release 1.88
Add commons-logging jar to module dependencies.
Add commons-logging to MergeVcfs and SplitVcfs executable jars so that outputting BCF format works.
For non-demultiplex mode, don't require barcode files.