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.