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orangeSi / bam2msa

convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region
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empty output #2

Open parlar opened 1 year ago

parlar commented 1 year ago

Thank you for creating bam2msa. When trying out on my own data, the output is empty. The test data in the repo works fine though and there are no error messages.

I'm trying make an msa for a region that is quite long into the bam file, at about 940,000 in my bacterial genome.

Is it a bug?

orangeSi commented 3 months ago

I just noticed this issue, sorry for that! can you give the command line you used? example bam2msa ref.fa out.bwa.bam NC_045512.2_1bp_to_1680bp:15-43 --output-format 2 > out.xls. And if use column for big dataset, will waste much time.

orangeSi commented 3 months ago

I just now updated the master branch， it should work now。 but will cost much time for quite long region example 940kb

orangeSi commented 3 months ago

I use E.coli genome as reference, and use wgisum to simulator 100x PE 150 read. Then test the run time: for 1kb or 2kb region, bam2msa cost 1-2s, but for 10kb region, bam2msa will cost 180s .