Description
Append the minimap2's CS tag to SAM file.
If the CS tag is already present, this command will overwrite the existing tag.
⚠️ 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
| sam2paf | calcs | |
|---|---|---|
| Speed | + | - |
| Report substitution | + (if SAM includes MD tag) | + |
| Report CS tag | + (if SAM includes MD tag) | + |
| Output format | PAF | SAM or PAF |
1 maintainer
Metadata
1 maintainer
Release files for calcs 0.0.0.9999
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| calcs-0.0.0.9999.tar.gz | 7.9 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| calcs-0.0.0.9999-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 17.7 kB
Release files / calcs-0.0.0.9999.tar.gz
| Download URL | calcs-0.0.0.9999.tar.gz |
|---|---|
| Size | 7.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/0.0.0 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.7
|
Release files / calcs-0.0.0.9999-py3-none-any.whl
| Download URL | calcs-0.0.0.9999-py3-none-any.whl |
|---|---|
| Size | 9.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/0.0.0 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.7
|
Security for calcs 0.0.0.9999
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