Closed mkostich closed 9 months ago
You can't reproduce it without setting the --preset
option, as pointed out in 622. The preset sets those minimap2 parameters that aren't exposed to CLI: https://github.com/PacificBiosciences/pbmm2/blob/f7cbb14ababd959a29fa8410f5e79876111768d4/src/MM2Helper.cpp#L300
But from the code you can also see that you can override the preset defaults: https://github.com/PacificBiosciences/pbmm2/blob/f7cbb14ababd959a29fa8410f5e79876111768d4/src/MM2Helper.cpp#L335-L361
Sorry I could not figure out how to reopen issue 622, to which this is directly related.
Operating system Debian GNU/Linux 11 (bullseye)
Package name
Conda environment
Describe the bug Comparing:
To:
With the explicit parameters I get:
While with
--preset ISOSEQ
I get:Note that edit distance is longer, and mapq is lower for intron-containing alignments with explicit parameters than it is with
--preset ISOSEQ
. For those sequences, with--preset ISOSEQ
we have many insertions in cigar string, while corresponding locations with explicit parameters instead have similar number/position of deletions. For the last sequence the results are identical. One distinguishing feature of the last sequence mapping is that it does not involve large gaps/introns (hint).As far as I can tell from the documentation, what I can glean from code, and answers previously provided in this forum, the two commands should produce very comparable, if not identical outputs. I would like to figure out what I am doing wrong (am I missing a parameter?), or point out something the code may be doing wrong, or encourage more explicit documentation on this subject. Please note, this behavior has been reproduced with pbmm2 from the official smrttools 11.1 (
https://downloads.pacbcloud.com/public/software/installers/smrtlink_11.1.0.166339.zip
) and 12.0 (https://downloads.pacbcloud.com/public/software/installers/smrtlink_12.0.0.177059.zip
) releases as well.Error message
The runs complete without reporting an error.
To Reproduce
First command is:
Second command is:
GRCh38.primary_assembly.genome.fa
can be downloaded here:https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz
.The
gather.test3.fasta
file, which I renamedgather.test3.fasta.txt
in order to upload (weird thing w/ my work laptop), which contains 5 sequences, is attached.Expected behavior
Using the parameter equivalency to presets provided in documentation should result in similar or identical behavior to using the corresponding preset. Thanks for your help!!! gather.test3.fasta.txt