This is the command gt-compreads-refcompress that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gt-compreads-refcompress - Generates compact encoding for fastq data using Reference
Compressed Reads (RCR).
SYNOPSIS
gt compreads refcompress [option ...] (-bam file -ref file)
DESCRIPTION
-v [yes|no]
be verbose (default: no)
-mquals [yes|no]
store mapping quality for each read (default: no)
-quals [yes|no]
store all quality values for each read, this implies enabling of option "vquals"
(default: no)
-vquals [yes|no]
store quality values of read positions having variations compared to reference
(default: no)
-descs [yes|no]
store read name for each read (default: no)
-ureads [yes|no]
store unmapped reads in a separated fastq file (base name will be the value given in
name and suffix will be " _unmapped.fastq" (default: no)
-ref [string]
Index file (generated by the gt encseq tool) for reference genome. (default:
undefined)
-bam [string]
File containing alignment of reads to genome (sorted ".bam" file). (default:
undefined)
-name [string]
specify base name for RCR to be generated. If not set, base name will be set to base
name of value given for option "bam" (default: undefined)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to <gt-users@genometools.org>.
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