Summarizer usage

Summarizer

There are four required positional arguments:

serratus_summarizer_flom.py InputSamFileName MetaTsvFilename SummaryFileName OutputSamFileName

There is one tsv file with metadata, one line per accession with fields:

1. accession
2. length
3. name
4. family
5. offset of fragment vs. full-length genome, or 0
6. Pan-genome length

MK581208.1 28074 Infectious bronchitis virus Coronaviridae 0 30000

Example for pipe:

serratus_summarizer_flom.py /dev/stdin ~/flom1.sumzer.tsv DRR123456.summary /dev/stdout

The SUMZER_COMMENT environment variable is written to the first line of the output file if set.