bam2emase error when reference is not defined "*"

[dantaki]

For reads like these:

NS500146:205:H2WC7BGX2:1:11101:6081:1104	141	*	0	0	*	*	0	0	GTGGAGAGATCCAGGGATGGGAATCTCAGGACAATTAACCTGGACCAGACTCCCACAGGGTTTCAAAAACAGTCCC	AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE	XM:i:0

I get this error when running bam2emase

(gbrs) $ gbrs bam2emase -i test.bam -m R84-REL1505/ref.transcripts.info  -s A,B,C,D,E,F,G,H -o test.emase

Traceback (most recent call last):
  File "anaconda3/envs/gbrs/bin/gbrs", line 4, in <module>
    __import__('pkg_resources').run_script('gbrs==0.1.5', 'gbrs')
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/pkg_resources/__init__.py", line 664, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1444, in run_script
    exec(code, namespace, namespace)
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/gbrs-0.1.5-py2.7.egg-info/scripts/gbrs", line 199, in <module>
    sys.exit(main())
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/gbrs-0.1.5-py2.7.egg-info/scripts/gbrs", line 195, in main
    args.func(**kws)
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/gbrs/emase_utils.py", line 101, in bam2emase
    alignmat_factory.prepare(haplotypes, loci, outdir=os.path.dirname(outfile))
  File "anaconda3/envs/gbrs/lib/python2.7/site-packages/emase/AlignmentMatrixFactory.py", line 48, in prepare
    locus, hap = fh.getrname(aln.tid).split(delim)
AttributeError: 'NoneType' object has no attribute 'split'

I fixed the error by adding this line above line 48 in AlignmentMatrixFactory.py

                if aln.flag != 4 and aln.flag != 8:
                    if aln.tid==-1: continue
                    locus, hap = fh.getrname(aln.tid).split(delim)

These were the commands I used before on a small test case

$ bowtie -q -a --best --strata --sam -v 3 bowtie_ref/transcripts -1 fq/PB357_04_NPC-44200414_R1.fastq.gz -2 fq/PB357_04_NPC-44200414_R2.fastq.gz | samtools view -bS - > test.bam

$ gbrs bam2emase -i test.bam -m /oasis/projects/nsf/ddp195/dantakli/organoid/R84-REL1505/ref.transcripts.info -s 1,2,3,4,5,6,7,8 -o test.emase

Thanks!

[dantaki]

Also I believe to compare the bitwise flags this is the proper method

def is_unmapped(flag):
    if flag & 4 or flag & 8: return True
    else: return False

so now is_unmapped(143) will return True and you can skip it