Eric Banks ae08d35138 Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).		2012-07-18 12:57:34 -04:00
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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	Throwing UnknownTribbleType exception instead of CommandLineException when an unknown tribble type is specified.	2012-06-28 11:28:04 -04:00
gatk	Catch 'too many open files' errors that show up when trying to read the bam index. All that needs to be done is to flesh out the original error message (because it will get caught later and rethrown correctly).	2012-07-18 12:57:34 -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