calcs 0.0.0.9999

Description

Append the minimap2's CS tag to SAM file.
If the CS tag is already present, this command will overwrite the existing tag.

:warning: This tool will be maintained until the samtools team implements official CS caller.

Installation

You can install calcs using pip:

pip install calcs

Usage

calcs [options] <in.sam> -r/--reference <in.fasta>

Getting Started

# CS tag (short form)
calcs aln.sam -r ref.fasta > aln_cs.sam
# CS tag (long form)
calcs aln.sam -r ref.fasta -l > aln_cslong.sam
# PAF format with CS tag (short form)
calcs aln.sam -r ref.fasta -p > aln_cs.paf
# PAF format with CS tag (long form)
calcs aln.sam -r ref.fasta -p -l > aln_cslong.paf
# Multithreading
calcs aln.sam -r ref.fasta -t 4 > aln_cs.sam

Options

-l, --long: output the cs tag in  the long form
-t, --threads INT: number of threads to use (default: 1)

Examples

calcs examples/example.sam -r examples/ref.fa > example_cs.sam

If the input file is a BAM/CRAN format, you can use samtools view.

samtools view examples/example.bam |
  calcs -l -r examples/ref.fa |
  samtools sort > example_cslong.bam

paftools.js sam2paf vs calcs