command line help is cryptic

[dbrami]

Hi, I have used bam2fastq on a bam file containing ONLY unaligned reads (bit flags are either 77 or 141) with following command: bam2fastq -o C14IAWNRP1#.fastq C14IAWNRP1.trimmed.noplant.bam

It has output all the reads in the bam file to fastq (which is exactly what I wanted but hoping to understand the params better) --aligned --no-aligned Reads in the BAM that are aligned will (will not) be extracted. [Default: extract aligned reads] --unaligned --no-unaligned Reads in the BAM that are not aligned will (will not) be extracted. the "will (will not)" descriptions are pretty confusing and there seems to be contradicting default behaviors described.

Otherwise works fine :)

[jts]

I agree this is confusing. I propose to get rid of the --aligned and --unaligned options, since they are the default behaviour. The options will be --no-aligned and --no-unaligned, which will suppress writing out aligned/unaligned reads. It will simplify the help message.

What do you think?

[Naibin]

@jts
Agree！！！ I have tried to extracted reads from a bam file
I FOUND when using --aligned option actually un-mapped reads was extracted when I was using --no-unaligned ,this will work .