usage: tgStoreDump -G <gkpStore> -T <tigStore> <v> [opts]
STORE SELECTION (mandatory)
-G <gkpStore> path to the gatekeeper store
-T <tigStore> <v> path to the tigStore, version, to use
TIG SELECTION - if nothing specified, all tigs are reported
- all ranges are inclusive.
-tig A[-B] only dump tigs between ids A and B
-unassembled only dump tigs that are 'unassembled'
-bubbles only dump tigs that are 'bubbles'
-contigs only dump tigs that are 'contigs'
-nreads min max only dump tigs with between min and max reads
-length min max only dump tigs with length between 'min' and 'max' bases
-coverage c C g G only dump tigs with between fraction g and G at coverage between c and C
example: -coverage 10 inf 0.5 1.0 would report tigs where half of the
bases are at 10+ times coverage.
DUMP TYPE - all dumps, except status, report on tigs selected as above
-status the number of tigs in the store
-tigs a list of tigs, and some information about them
-consensus [opts] the consensus sequence, with options:
-gapped report the gapped (multialignment) consensus sequence
-fasta report sequences in FASTA format (the default)
-fastq report sequences in FASTQ format
-layout [opts] the layout of reads in each tig
if '-o' is supplied, three files are created, otherwise just the layout is printed to stdout
-gapped report the gapped (multialignment) positions
-o outputPrefix write plots to 'outputPrefix.*' in the current directory
-multialign [opts] the full multialignment, output is to stdout
-w width width of the page
-s spacing spacing between reads on the same line
-sizes [opts] size statistics
-s genomesize denominator to use for n50 computation
-coverage [opts] read coverage plots, one plot per tig
-o outputPrefix write plots to 'outputPrefix.*' in the current directory
-depth [opts] a histogram of depths
-single one histogram per tig
-overlap read overlaps
-thin overlap report regions where the (thickest) read overlap is less than 'overlap' bases
-overlaphistogram a histogram of the thickest overlaps used
-o outputPrefix write plots to 'outputPrefix.*' in the current directory