fromsam
Usage: recs fromsam <args> [<files>] Each line of input (or lines of <files>) is parsed as a SAM (Sequence Alignment/Map) formatted record to produce a recs output record. To parse a BAM file, please pipe it from `samtools view file.bam` into this command. The output records will contain the following fields: qname flag rname pos mapq cigar rnext pnext tlen seq qual Additional optional SAM fields are parsed into the "tag" key, which is a hash keyed by the SAM field tag name. The values are also hashes containing a "type" and "value" field. For example, a read group tag will end up in your record like this: tags => { RG => { type => "Z", value => "...", } } Refer to the SAM spec for field details: http://samtools.github.io/hts- specs/SAMv1.pdf Arguments: --flags Decode flag bitstring into a "flags" hashref --quals Decode qual string into a "quals" array of numeric values --filename-key|fk <keyspec> Add a key with the source filename (if no filename is applicable will put NONE) Help Options: --help This help screen Examples: Parse SAM and calculate average mapping quality: recs fromsam input.sam | recs collate -a avg,mapq Parse BAM: samtools view input.bam | recs fromsam Parse SAM pre-filtered by read group: samtools view -r SAMPLE-1234 input.sam | recs fromsam The same, but probably slower: recs fromsam input.sam | recs grep '{{tag/RG/value}} eq "SAMPLE-1234"'
App::RecordStream::Bio
To install App::RecordStream::Bio, copy and paste the appropriate command in to your terminal.
cpanm
cpanm App::RecordStream::Bio
CPAN shell
perl -MCPAN -e shell install App::RecordStream::Bio
For more information on module installation, please visit the detailed CPAN module installation guide.