Provided by: genometools_1.5.1-2ubuntu1_amd64 bug


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


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


           be verbose (default: no)

           store mapping quality for each read (default: no)

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

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

           store read name for each read (default: 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)

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

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

           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 <>.

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