gustaf(1) on Linux
The text fd9e8d696715, as Debian 9 (Stretch) shipped it.
Gustaf - Generic mUlti-SpliT Alignment Finder: Tool for split-read mapping allowing multiple splits. SYNOPSIS DESCRIPTION REQUIRED ARGUMENTS OPTIONS -h, --help --version-check BOOL --version -tp, --transPen INTEGER -ip, --invPen INTEGER -op, --orderPen INTEGER -oth, --overlapThresh DOUBLE -gth, --gapThresh INTEGER -ith, --initGapThresh INTEGER -bth, --breakendThresh INTEGER -tth, --tandemThresh INTEGER -pth, --breakpoint-pos-range INTEGER -cbp, --complex-breakpoints -st, --support INTEGER -mst, --mate-support INTEGER -ll, --library-size INTEGER -le, --library-error INTEGER -rc, --revcompl -m, --matchfile INPUT_FILE -gff, --gffOut OUTPUT_FILE -vcf, --vcfOut OUTPUT_FILE -j, --jobName STRING -do, --dots -nth, --numThreads INTEGER -e, --epsilon DOUBLE -l, --minLength INTEGER -f, --forward -r, --reverse -a, --alphabet STRING -v, --verbose -k, --kmer INTEGER -rp, --repeatPeriod INTEGER -rl, --repeatLength INTEGER -c, --abundanceCut DOUBLE -x, --xDrop DOUBLE -vs, --verification STRING -dt, --disableThresh INTEGER -n, --numMatches INTEGER -s, --sortThresh INTEGER VERSION