missing quality values stop certain tools

[tolot27]

If a sam/bam file contains alignments without quality values (column 11 = *), certain tools (i. e. bamtofastq) stop at those alignments and do not produce any futher output. No error message is reported.

A typical sam/bam file without quality values can be produced by mapping fasta sequences to a reference instead of fastq sequences.

[tolot27]

The root cause of the issue is https://github.com/arq5x/bedtools2/blob/master/src/utils/BamTools/include/BamAlignment.hpp#L182 where an invalid quality score is assigned to each position during loading of the alignment.