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.\"     Title: gt-compreads-refcompress
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 10/25/2023
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-COMPREADS\-REFCO" "1" "10/25/2023" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-compreads-refcompress \- Generates compact encoding for fastq data using Reference Compressed Reads (RCR)\&.
.SH "SYNOPSIS"
.sp
\fBgt compreads refcompress\fR [option \&...] (\-bam file \-ref file)
.SH "DESCRIPTION"
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-mquals\fR [\fIyes|no\fR]
.RS 4
store mapping quality for each read (default: no)
.RE
.PP
\fB\-quals\fR [\fIyes|no\fR]
.RS 4
store all quality values for each read, this implies enabling of option "vquals" (default: no)
.RE
.PP
\fB\-vquals\fR [\fIyes|no\fR]
.RS 4
store quality values of read positions having variations compared to reference (default: no)
.RE
.PP
\fB\-descs\fR [\fIyes|no\fR]
.RS 4
store read name for each read (default: no)
.RE
.PP
\fB\-ureads\fR [\fIyes|no\fR]
.RS 4
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)
.RE
.PP
\fB\-ref\fR [\fIstring\fR]
.RS 4
Index file (generated by the gt encseq tool) for reference genome\&. (default: undefined)
.RE
.PP
\fB\-bam\fR [\fIstring\fR]
.RS 4
File containing alignment of reads to genome (sorted "\&.bam" file)\&. (default: undefined)
.RE
.PP
\fB\-name\fR [\fIstring\fR]
.RS 4
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)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.