NAME

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

SYNOPSIS

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

OPTIONS

       -v
           be verbose (default: no)

       -mquals
           store mapping quality for each read (default: no)

       -quals
           store all quality values for each read, this implies enabling of option "vquals"
           (default: no)

       -vquals
           store quality values of read positions having variations compared to reference
           (default: no)

       -descs
           store read name for each read (default: no)

       -ureads
           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
           Index file (generated by the gt encseq tool) for reference genome. (default:
           undefined)

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

       -name
           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

AUTHOR

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

                                            10/07/2012                      GT-COMPREADS-REFCO(1)