2.11.0 --externalaligner causes error #475
Description
Using the --externalaligner option results in an error when executing SoftClipsToSplitReads:
ERROR: Invalid argument '--ALIGNER_COMMAND_LINE'.
I'm not completely confident this is the cause, but all the other args for this command only have a single leading -.
The command from the log (I've wrapped the command on those args):
SoftClipsToSplitReads -TMP_DIR tmp/test.assembly.bam.gridss.working/ -WORKING_DIR tmp -REFERENCE_SEQUENCE ref/genome.fa -WORKER_THREADS 8 -I out/test.assembly.bam -O tmp/test.assembly.bam.gridss.working/tmp.test.assembly.bam.sc2sr.primary.sv.bam -OUTPUT_UNORDERED_RECORDS tmp/test.assembly.bam.gridss.working/tmp.test.assembly.bam.sc2sr.supp.sv.bam -REALIGN_ENTIRE_READ true -READJUST_PRIMARY_ALIGNMENT_POSITION true
--ALIGNER_COMMAND_LINE null
--ALIGNER_COMMAND_LINE bwa
--ALIGNER_COMMAND_LINE mem
--ALIGNER_COMMAND_LINE -K
--ALIGNER_COMMAND_LINE 10000000
--ALIGNER_COMMAND_LINE -L
--ALIGNER_COMMAND_LINE 0,0
--ALIGNER_COMMAND_LINE -t
--ALIGNER_COMMAND_LINE %3$d
--ALIGNER_COMMAND_LINE %2$s
--ALIGNER_COMMAND_LINE %1$s