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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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EstimateReadCountPerWindow.py IndexError #14

Closed damientully closed 7 years ago

damientully commented 7 years ago

Hi Chris,

I am getting the following error with using the script EstimatedReadCountPerWindow.py

python2.7 tools/EstimateReadCountPerWindow.py InputFileList.csv Now counting read and insert sizes for 25236 Traceback (most recent call last): File "tools/EstimateReadCountPerWindow.py", line 152, in <module> start = min(MappedPositions[0], MappedPositions[-1]) IndexError: list index out of range

Any suggestions. I emailed a subset of reads.

Thanks, Damien

ChrisHIV commented 7 years ago

Hi Damien, I haven't got your reads yet but I'm pretty sure what I just pushed will correct the bug. Pull and try again. Thanks for spotting!

damientully commented 7 years ago

Hi Chris,

Thanks for the speedy reply. It does produce .csv but Now counting read and insert sizes for 25236 Info: 123 of 102722 reads in 2733.bam are flagged as being paired but don't have a mate present. Traceback (most recent call last): File "tools/EstimateReadCountPerWindow.py", line 282, in <module> alias = aliases[(i - 1) % 2] IndexError: list index out of range

Damien

ChrisHIV commented 7 years ago

D'oh. Try again?

damientully commented 7 years ago

Wonderful! That worked! Produced both pdf and .csv.

Cheers, Damien