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 https://github.com/genometools/genometools/issues.