How to output all sequences with bwa mem, not `*`? I've been running bwa mem -a for alignment, using the -a flag---this will 


  output all alignments for SE or unpaired PE


I've noticed in the SAM that there are several alignments with * in the SEQ and QUAL fields. Based on the documentation:


  
  SEQ: segment SEQuence. This field can be a ‘*’ when the sequence is not stored. If not a ‘*’, the length of the sequence must equal the
  sum of lengths of M/I/S/=/X operations in CIGAR. An ‘=’ denotes the
  base is identical to the reference base. No assumptions can be made on
  the letter cases.
  QUAL: ASCII of base QUALity plus 33 (same as the quality string in the Sanger FASTQ format). A base quality is the phred-scaled base
  error probability which equals −10 log10 Pr{base is wrong}. This field
  can be a ‘*’ when quality is not stored. If not a ‘*’, SEQ must not be
  a ‘*’ and the length of the quality string ought to equal the length
  of SEQ.
  


it appears the sequence isn't stored. 

I would strongly prefer to have the sequence in this case. Is there any to direct bwa to output these sequences?
I don't believe that is an option.  Internally we created a patch and submitted it to BWA however that was 4 years ago and it has not been accepted.