Hi group, 

Just a quick question, how to I properly use the fastq command in samtools 1.3? According to the documentation I should be doing this:

    samtools fastq -On -s ion36_nohost.fastq ion36_nohost.bam

 but the result is this:

    [M::bam2fq_mainloop_singletontrack] discarded 0 singletons
    
    [M::bam2fq_mainloop_singletontrack] processed 0 reads

I'm trying to get the unmapped reads. My bam file does contain the reads in question but I'm doing something wrong since they switched to `fastq` from `bam2fq` 

Any idea? 
I must have misunderstood the docs becasue this was at the top and works

    samtools fastq input.bam > output.fastq

but the detail doc is different here:

> samtools fastq [options] in.bam  samtools fasta [options] in.bam
> 
> Converts a BAM or CRAM into either FASTQ or FASTA format depending on
> the command invoked.
> 
> OPTIONS:
> 
> -n By default, either '/1' or '/2' is added to the end of read names where the corresponding BAM_READ1 or BAM_READ2 flag is set. Using -n
> causes read names to be left as they are.
> 
> -O Use quality values from OQ tags in preference to standard quality string if available.
> 
> -s FILE Write singleton reads in FASTQ format to FILE instead of outputting them.
> 
> -t Copy RG, BC and QT tags to the FASTQ header line, if they exist.
> 
> -1 FILE Write reads with the BAM_READ1 flag set to FILE instead of outputting them.
> 
> -2 FILE Write reads with the BAM_READ2 flag set to FILE instead of outputting them.
> 
> -0 FILE Write reads with both or neither of the BAM_READ1 and BAM_READ2 flags set to FILE instead of outputting them.
> 
> -f INT Only output alignments with all bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e.
> /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/)
> [0].
> 
> -F INT Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x'
> (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e.
> /^0[0-7]+/) [0].