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 with0' (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 with0' (i.e. /^0[0-7]+/) [0].