-u always active, unaligned reads cause parse error in samtools

[jmcasc]

At the moment, RapMap always prints unaligned reads, even if the -u flag is not given. The writeUnmapped variable seems to be set according to the flag, but is later ignored. Whenever such an unaligned read entry is read by samtools for sam->bam conversion, samtools terminates with a "parse error on line xxxxx".

Happens on current master branch and with current samtools version.

[mflevine]

Yea, writeUnmapped variable is never used or checked.

[shengxingou]

At the moment, RapMap always prints unaligned reads, even if the -u flag is not given. The writeUnmapped variable seems to be set according to the flag, but is later ignored. Whenever such an unaligned read entry is read by samtools for sam->bam conversion, samtools terminates with a "parse error on line xxxxx".

Happens on current master branch and with current samtools version.

I have encountered the same problem. I found that changing the eighth column of the Sam file to 0 can solve this problem. But I don't know why that's the case. "rapmap quasimap -i newest_ref_index -1 <(gunzip -c R1.fq.fastp.gz) -2 <(gunzip -c R2.fq.fastp.gz) -t 10 -u -o test.sam cat test2.sam|awk '{if ($8 == "") $8 = "0"; print}' OFS='\t'|samtools view -@ 10 -bS -f 12 > test.sam.f12.bam"