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haowenz / chromap

Fast alignment and preprocessing of chromatin profiles
https://haowenz.github.io/chromap/
MIT License
192 stars 21 forks source link

Output unsorted SAM #97

Open baozg opened 2 years ago

baozg commented 2 years ago

Hi, Haowen

Chromap is super fast when I use pair format. But I want to use chromap for assembly scaffolding pipeline (chromap + yahs), espeically for large plant genome. Since yahs accept the bam only, I use the chromap mapping with --SAM, but output SAM occupy more than half time. If I use juicer pipeline (split fastq + bwa mem + awk + perl), since the fully parallel, its speed is very comparable with chromap. Most pipeline designed for BAM, so I have to use bam (https://github.com/c-zhou/yahs/issues/14)

I found the SAM output use about only 1 thread, can we output unosorted SAM first? I thinkc chromap is trying to use temp file and convert it to sorted SAM. For performance, it seems that samtools convert and sort may be better?

Best regards Zhigui

haowenz commented 2 years ago

Currently Chromap sorts the output mappings by default. We didn't leave an option to turn it off, which means we cannot do this right now without changing the code. We will add one option to turn off the sorting by default in the next release.

baozg commented 2 years ago

That's so great. Is the output sorted by read name? Another behavior is that chromap merge all the output after mapping. Count it can directly output to the stdout when require the SAM output, then it can directly pipe it to samtools for coverting.

haowenz commented 2 years ago

The mappings are sorted by mapping positions. You may try -o /dev/stdout and see if the mappings are output into stdout. If yes then you might be able to pipe things up.