EricKutschera
commented
3 months ago Was the ESPRESSO output that you ran create_corrected_sam.py on created from ESPRESSO v1.5.0? In v1.4.0 it was expected to see a value like 639.5 in that part of a read_final file. In v1.5.0 it should always be an integer. In v1.4.0 the value wasn't really being used for anything, but in v1.5.0 the way that value was calculated was updated so that create_corrected_sam.py could use it
This is where the code creates that line of the output: https://github.com/Xinglab/espresso/blob/v1.5.0/src/ESPRESSO_C.pl#L1332
The 639.5 would be from $read_pos_matched_to_sj which should always be an integer because it's based on $query_sj_pos which is an alignment position: https://github.com/Xinglab/espresso/blob/v1.5.0/src/ESPRESSO_C.pl#L1874
In v1.4.0 that value came from $est_pos_read which was a midpoint of two coordinates: https://github.com/Xinglab/espresso/blob/v1.4.0/src/ESPRESSO_C.pl#L1608
junior-2016
hi, eric. when I run create_corrected_sam.py script, an error occurs during the conversion of a string to an integer:
I reviewed the corresponding records in the file, and they are as follows:
One of the columns = ['0f318797-64b5-4330-916e-f51c1afe079b', 'SJ', '3', 'chr9:16056:16717:1', '638', '716', 'corrected', 'chr9:16061:16717:1', '639.5', '714.5', '7.21455013503734e-06', 'no', 'no'] contains the value '639.5', which should have been an integer. Is this case expected behavior?