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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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Unexpected attribute properties for pysam.AlignedSegment #11

Closed damientully closed 7 years ago

damientully commented 7 years ago

Hi Chris,

I am getting the following error on a bam file when running ./phyloscanner_make_trees.py

Unexpected attribute properties for pysam.AlignedSegment
 M03475:62:000000000-B2RNP:1:2110:11349:14877   165 0   301 0   None    0   301 8   ATGCCGTC    array('B', [35, 35, 37, 37, 37, 34, 35, 35])    [('RG', 'ZY6QANZF1GE'), ('ZA', '<&;0;0;;2;12S7M1I77M;2T6C75><@;0;0;;0;;>')] 
Quitting

I just emailed you a sample of the reads. Many thanks, Damien

ChrisHIV commented 7 years ago

Hi Damien, I'm on holiday at the moment and at a conference next week; I'll try to find time to look at it during the conference. Cheers

damientully commented 7 years ago

Great thanks Chris!

ChrisHIV commented 7 years ago

Hi Damien, thanks for catching that. Pull the code and try again.

damientully commented 7 years ago

Hi Chris,

Appears to be working now.

Thanks! Damien