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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Signed Integer Overflow in MAPQ Computation #95

Open paudano opened 3 years ago

paudano commented 3 years ago

I am getting negative MAPQ numbers from ngmlr. I noticed this when samtools failed converting SAM to CRAM. This looks to me like 32-bit signed integer overflow on some astronomically high MAPQ?

ngmlr version 0.2.7

Command: ngmlr -t 12 -r ${REF} -q chr13-112318733-INS-3060.fa.gz -o HG00733_flank-500_sv_ins.sam

I am aligning against this reference (hg38, primary assembly only): ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/

I am attaching the input FASTA and aligned SAM (gzipped since I can BAM/CRAM it).

chr13-112318733-INS-3060.fa.gz chr13-112318733-INS-3060.sam.gz

monsanto-pinheiro commented 3 years ago

Please, check the fix in #96