gustaf(1) on Linux
The text 0ef104bc44a9, as Debian 8 (Jessie) shipped it.
Gustaf - Generic mUlti-SpliT Alignment Finder: Tool for split-read mapping allowing multiple splits. SYNOPSIS DESCRIPTION -h, --help --version -tp, --transPen INT -ip, --invPen INT -op, --orderPen INT -oth, --overlapThresh DOUBLE -gth, --gapThresh INT -ith, --initGapThresh INT -st, --support INT -m, --matchfile FILE -bpo, --breakpointOut FILE -j, --jobName STR -do, --dots -e, --epsilon NUM -l, --minLength NUM -f, --forward -r, --reverse -a, --alphabet STR -v, --verbose -k, --kmer NUM -rp, --repeatPeriod NUM -rl, --repeatLength NUM -c, --abundanceCut NUM -x, --xDrop NUM -vs, --verification STR -dt, --disableThresh NUM -n, --numMatches NUM -s, --sortThresh NUM VERSION