Changes made by latest IntelliJ.
Add SeekableHTTPStream ctor that takes a Proxy object.
Converted to use arrays internally to reduce runtime by 30-40%.
Adding functionality to SamToFastq to optionally trim read 1 or read 2 and to optionally write a maximum number of bases (post-trimming) to the fastq file.
Added a new utility called ReorderSam (contributed by Mark DePristo) which is designed to take a SAM/BAM file and switch out the sequence dictionary for one in a different order, and then re-order the INPUT file to produce a coordinate sorted OUTPUT file with respect to the new sequence dictionary.
Added a new utility to add or replace the (possibly empty) set of read groups in an existing SAM or BAM file, contributed by Mark DePristo.
Modified AbstractAlignmentMerger and SamAlignment merger to handle (a) multiple files of alignments and (b) separate alignments of both ends of a paired read
Added a todo
Moved AddOrReplaceReadGroups from test to java folder
Eliminate test that relied on large BAM stored on SF.
SF release 1.41
Significant refactoring of MergeBamAlignment.  AbstractAlignmentMerger and SamAlignmentMerger have been modified to use the expected orientations of read pairs rather than a boolean for whether the library is a jumping library.  They have new constructors and code that uses these directly will have to be modified to use them.  MergeBamAlignment has retained JUMP_SIZE for backwards compatiblity, but it has been deprecated and uses should switch to providing EXPECTED_ORIENTATIONS.
Reverse complement all reads with the negativeStrandFlag set, even if they are unmapped
PIC-482 -- Make sure BAM index is created when indexing on the fly, even when the output BAM does not contain any reads.
Added a method to get the size, in bytes, of a file or directory tree.
minor bug fix
Fix bug in refactored AbstractAlignmentMerger
Added IoUtil.fileSuffix
Fixed compilation error
PIC-483 Flush output stream so that message that error list has been truncated is emitted.