2.11.0 --externalaligner causes error

[keiranmraine]

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

[keiranmraine]

I've just noticed that SoftClipsToSplitReads is in the logs twice, incase this is relevant. The first doesn't have any ALIGNER_COMMAND_LINE options, the second being the one that fails.

**********    SoftClipsToSplitReads -TMP_DIR tmp -WORKING_DIR tmp -REFERENCE_SEQUENCE ref/genome.fa -I tmp/test.bam.gridss.working/tmp.test.bam.coordinate.bam -O tmp/test.bam.gridss.working/tmp.test.bam.sc2sr.primary.sv.bam -OUTPUT_UNORDERED_RECORDS tmp/test.bam.gridss.working/tmp.test.bam.sc2sr.supp.sv.bam -WORKER_THREADS 8
**********    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

[keiranmraine]

Looking at the comparison runs I'm running for 2.9.4 and 2.10.2 the additional - is the cause.