gt-compreads-refcompress(1)
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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