Question: Why Import Command In Samtools Is Not Shown In The Short Help Of Samtools?
3
gravatar for Pablo Marin-Garcia
7.4 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

I am converting sam to bam using 'samtools import' command.

I am curious why if I do 'samtools' I can not see the 'import' command?

Program: samtools (Tools for alignments in the SAM format) Version: 0.1.13 (r926:134)

Usage: samtools <command/> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         pileup      generate pileup output
         mpileup     multi-way pileup
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         glfview     print GLFv3 file
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes

If I do samtools import it says:

 $  samtools import
Usage: bamtk import <in.ref_list> <in.sam> <out.bam>

I find out the samtools import time ago by chance in a blog (unable to find it in any samtools doc [is it there? where?]), until then I was doing it with a less concise command:

samtools view -bt ref.fa.fai aln.sam > aln.bam

Why is import command not documented in the samtools help? Why samtools import usage talk about bamtk?

samtools • 4.6k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 7.4 years ago by Pablo Marin-Garcia1.8k
4
gravatar for Pablo Marin-Garcia
7.4 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

This is as far I went to answer myself:

I have seen at samtools code that all other samtools commands have a bam_[?]command[?].c execpt import and that there is a bamtk.c.

bamtk.c has the command help also with no imoport

[?]

But then in the argument parsing the first one is import

[?]

[?]

==update==

[?]

2009 man page

[?]

But in the latest man pages does not have the import command but, in view option -t still have the old wording referencing to the import command.

[?]

So seems that import command is not longer supported and functionality has been passed to view -bt

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Pablo Marin-Garcia1.8k
5

I believe import was deprecated over a year ago in favor of view.

ADD REPLYlink written 7.4 years ago by Aaronquinlan10k

@aaronQuinlan, I compiled samtools manually and didn't put the manpages. Looking to a man pae over internet: COMMANDS AND OPTIONS import samtools import [?] [?] [?]

             Since 0.1.4, this command is an alias of:

             samtools view -bt <in.ref_list> -o <out.bam> <in.sam>

http://www.genome.iastate.edu/bioinfo/resources/manuals/rna_bowtie.samtools.txt (2009)

ADD REPLYlink written 7.4 years ago by Pablo Marin-Garcia1.8k
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