ValueError: invalid coordinates: start > stop

[pauline-ng]

Hi Adam,

I'm getting the following error that breaks BamSurgeon addsv.py:

Traceback (most recent call last):
  File "/usr/local/bin/addsv.py", line 4, in <module>
    __import__('pkg_resources').run_script('bamsurgeon==1.2', 'addsv.py')
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 665, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1470, in run_script
    exec(script_code, namespace, namespace)
  File "/usr/local/lib/python3.8/dist-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsv.py", line 1305, in <module>
  File "/usr/local/lib/python3.8/dist-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsv.py", line 1100, in main
  File "/usr/local/lib/python3.8/dist-packages/bamsurgeon-1.2-py3.8.egg/EGG-INFO/scripts/addsv.py", line 389, in fetch_read_names
  File "pysam/libcalignmentfile.pyx", line 1082, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (48025033) > stop (48024294)

As far as I can tell, this happens when the upstream altered region overlaps the downstream altered region.

INFO 2021-02-04 02:32:18,364 fetched 226 read pairs from 2:48021205-48025033, downsample factor: 0.500000
INFO 2021-02-04 02:32:18,371 fetched 250 read pairs from 2:48024294-48028525, downsample factor: 0.500000

where 48025033 > 4802494.

Some additional log info:

INFO 2021-02-04 02:32:18,333 2_48023033_48023033_BIGDEL start: 48021033, end: 48025033, tgtstart: 172, tgtend: 4000, refstart: 48021205, refend: 48025033
INFO 2021-02-04 02:32:18,346 2_48023033_48023033_BIGDEL alignment result: ['SUMMARY', '21146', '26', '4257', '0', '4231']
INFO 2021-02-04 02:32:18,347 2_48023033_48023033_BIGDEL trimmed contig length: 4231
INFO 2021-02-04 02:32:18,347 2_48023033_48023033_BIGDEL trn_start: 48024294, trn_end: 48032294, trn_tgtstart: 0, trn_tgtend:4231 , trn_refstart: 48024294, trn_refend: 48028525

Thanks,
Pauline

[adamewing]

There's a 5kbp size cutoff where addsv switches from big SV ("BIGDEL", "BIGINV", etc) mode to small SV mode ("DEL", "INV", etc) in an attempt to avoid this problem but it isn't a perfect solution obviously. Will look at detecting collisions between the big SV ends or turning this into a parameter.