Signed Integer Overflow in MAPQ Computation

[paudano]

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]

Please, check the fix in #96