Fix two issues in using bwa mem for alignments (#633)

* Fix bug in setting bwa mem options in --sensitive mode

* Remove alignment score filter on bwa mem

Based on bwa's definition of its alignment score, it
might be reasonable for it to output an alignment score
less than the specified `-T` value.

reports.py

@@ -746,7 +746,7 @@ def align_and_plot_coverage(
 
  bwa_opts = aligner_options.split()
  if sensitive:
- bwa_opts + "-k 12 -A 1 -B 1 -O 1 -E 1".split()
+ bwa_opts += "-k 12 -A 1 -B 1 -O 1 -E 1".split()
 
  # get the quality threshold from the opts
  # for downstream filtering

tools/bwa.py

@@ -156,29 +156,18 @@ def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None, min_qu
  readgroup_line = line
 
  assert len(readgroup_line) > 0
- 
- aln_bam_prefilter = util.file.mkstempfname('.prefiltered.bam')
+
+ tmp_bam_aligned = util.file.mkstempfname('.aligned.bam')
  # rather than reheader the alignment bam file later so it has the readgroup information
  # from the original bam file, we'll pass the RG line to bwa to write out
- self.mem(one_rg_inBam, refDb, aln_bam_prefilter, options=options+['-R', readgroup_line.rstrip("\n").rstrip("\r")], min_qual=min_qual, threads=threads)
+ self.mem(one_rg_inBam, refDb, tmp_bam_aligned, options=options+['-R', readgroup_line.rstrip("\n").rstrip("\r")], min_qual=min_qual, threads=threads)
 
  # if there was more than one RG in the input, we had to create a temporary file with the one RG specified
  # and we can safely delete it this file
  # if there was only one RG in the input, we used it directly and should not delete it
  if removeInput:
  os.unlink(one_rg_inBam)
 
- # @haydenm says: 
- # For some reason (particularly when the --sensitive option is on), bwa
- # doesn't listen to its '-T' flag and outputs alignments with score less
- # than the '-T 30' threshold. So filter these:
- if min_qual > 0:
- tmp_bam_aligned = util.file.mkstempfname('.aligned.bam')
- tools.samtools.SamtoolsTool().view(["-b", "-h", "-q", str(min_qual)], aln_bam_prefilter, tmp_bam_aligned)
- os.unlink(aln_bam_prefilter)
- else:
- shutil.move(aln_bam_prefilter, tmp_bam_aligned)
-
  # if the aligned bam file contains no reads after filtering
  # just create an empty file
  if tools.samtools.SamtoolsTool().count(tmp_bam_aligned) == 0: