Some refactoring. Fixed output for CdrBlast --cdr3-fastq-file option to produce gripped file based on file name suffix
Changed version in pom
Fixed bug in Util.isAvailable
Yet another minor fix
Refactoring continues
Some fixes (bad species for CdrBlastBatch and problems with temp file creation for CdrBlast) on the road
Allele id reporting in CdrBlast misc result files
A patch fixing error that occurs when using 0:1 read mask with batch CdrBlast
Removed .deleteOnExit() usage as it could result in too much open file handles (> default ulimit of 1024) for large number of samples and cores when calling CdrBlastBatch.
Several fixes
Added some missing V references.  Overlap tuning in Checkout, minor fix to CdrBlastBatch cli
Added option to skip output of reads with undefined barcode in Checkout. Added Duck and Chicken TRB reference (experimental). Minor fix to other references.
More accurate read overlapping in Checkout, added overlap parameters to CLI to increase execution flexibility. Added forced MIG size threshold and forced UMI collision filtering in AssembleBatch to increase execution flexibility.
Added chicken TRBJ reference
Fixed counting same UMI several times when multiple input files are provided for CdrBlast. It is now controlled with --same-sample option
Fix allowing only overlapped reads to be selected for assembly/cdr extraction.
Non-functional clonotype statistics report in FilterCdrBlastResults
Readme update
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pom version update