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parklab / bamsnap

MIT License
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ValueError: MD tag not present #5

Closed danielmsk closed 4 years ago

danielmsk commented 4 years ago 
Traceback (most recent call last):
  File "/home/mk446/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/mk446/anaconda3/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/mk446/anaconda3/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 436, in start_process_drawplot_bamlist
    imagefname = self.drawplot_bamlist(pos1, image_w, bamlist, xscale, refseq)
  File "/home/mk446/anaconda3/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 360, in drawplot_bamlist
    ia_sub = self.get_bamplot_image(bam, pos1, image_w, xscale, refseq)
  File "/home/mk446/anaconda3/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 257, in get_bamplot_image
    rset.calculate_readmap(is_strand_group=True)
  File "/home/mk446/anaconda3/lib/python3.7/site-packages/bamsnap/drawreadset.py", line 286, in calculate_readmap
    self.update_ref_seq_with_read(a)
  File "/home/mk446/anaconda3/lib/python3.7/site-packages/bamsnap/drawreadset.py", line 265, in update_ref_seq_with_read
    read_ref_seq = a.get_reference_sequence()
  File "pysam/libcalignedsegment.pyx", line 1833, in pysam.libcalignedsegment.AlignedSegment.get_reference_sequence
  File "pysam/libcalignedsegment.pyx", line 864, in pysam.libcalignedsegment.build_reference_sequence
ValueError: MD tag not present
danielmsk commented 4 years ago

https://github.com/parklab/bamsnap/commit/47a65c13e7436d212573f20b358a322b4f3ceaf3