Eric Banks 659eee13a6 Handle NPE generated in UG when non-standard reference bases are present in the fasta		2012-07-18 15:16:27 -04:00
..
alignment	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
commandline	Handle RuntimeExceptions thrown by Picard that are really User Errors. I will add unit tests for these as best I can later.	2012-07-18 13:56:35 -04:00
gatk	Handle NPE generated in UG when non-standard reference bases are present in the fasta	2012-07-18 15:16:27 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -04:00
utils	As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.	2012-07-17 22:18:43 -04:00