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gt-compreads-refcompress - Generates compact encoding for fastq data using Reference
Compressed Reads (RCR).


gt compreads refcompress [option ...] (-bam file -ref file)


-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:

-bam [string]
File containing alignment of reads to genome (sorted ".bam" file). (default:

-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)

display help and exit

display version information and exit


Report bugs to <gt-users@genometools.org>.

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