methratio.py error - Githubissues

What steps will reproduce the problem?
1.Run python methratio.py *.BSP > test.BSP 
2.
3.

What is the expected output? What do you see instead?
This script should generate output of summarized methylation calls for C's in 
the input.
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Instead, I get an following error message:
Mon Dec 19 10:44:32 2011: reading SRR019610.BSP ...
Traceback (most recent call last):
  File "/home2/ramamoor/softwares/bsmap-2.2/methratio.py", line 40, in ?
    map_info = get_alignment(line)
  File "/home2/ramamoor/softwares/bsmap-2.2/methratio.py", line 21, in get_alignment
    seq, strand, cr, pos, refseq = col[1], col[6][0], col[4], int(col[5]), col[8]
IndexError: list index out of range

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I closely looked at the .BSP file from bsmap and it looks like there are lines 
with only 4 columns. Here is an example from the BSMAP output file.
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SRR019489.60    AGAGGATTTTTAGAGATGGTGGAGAAATATAT    IIIIIIIIIII?IIIIIIIIIII?G3II<IDF    N
M 
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What version of the product are you using? On what operating system?

BSMAP v2.2 & RHEL 6.1
Please provide any additional information below.

Please let me know if I need to provide any additional information to fix this 
problem.

Thanks, Govind. BCM

Original issue reported on code.google.com by krgovind...@gmail.com on 19 Dec 2011 at 4:51

Shicheng-Guo / bsmap

methratio.py error #8