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jgurtowski / ectools

tools for error correction and working with long read data
BSD 3-Clause "New" or "Revised" License
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breaks while doing pre_delta_filter #4

Open yasirs opened 9 years ago

yasirs commented 9 years ago

When running correct.sh over some of my files, the pre_delta_filter.py breaks with the following message in the output:

+ FILTERED_DELTA=p0008.delta
+ [[ true == true ]]
+ FILTERED_DELTA=p0008.delta.pre
+ python /sw/ectools-master/pre_delta_filter.py p0008.delta 0.05 0.80 200 p0008.delta.pre
Traceback (most recent call last):
  File "/sw/ectools-master/pre_delta_filter.py", line 58, in <module>
    for record in getDeltaAlignmentIterator(fh):
  File "/sw/ectools-master/nucio.py", line 124, in getDeltaAlignmentIterator
    record = prepareDeltaRecord(itembuf)
  File "/swectools-master/nucio.py", line 111, in prepareDeltaRecord
    almnt.positions.append(int(buf[i]))
IndexError: list index out of range

I can send you the data privately if you wish.

jgurtowski commented 9 years ago

Yes, can you send along the delta file.