Spaces in segments file cause CdrBlast crash
fabio-t opened this issue · 0 comments
fabio-t commented
This line of code splits the segments file using a tab as separator, but sometimes there's no tab but a space.
I'm having a problem specifically with the file segments.all.txt
and this line:
MusMusculus TRB Variable TRBV7*01 289 TGAGGGCTCTAGCAGGCTCTGTCTTCTGACTTGTGGGACCTGTAAATTCCAGAGTCATGTAACCTGAAACCTCAAAGTCAAAGAATAGCTAGCAACTATGAAATAGTCCCTTCTCTCTGGACACCTCTCTGTGCTCTGGTACCAGAAGACCCTGGGCCCCAGTTCAATACTACAATAAAGAGGAGAAAGGAAGAGGAAATGTCCTTTATTCAATTTACAGCACACCAATTTGGTGACTAGCATCCTGAATTGAATCTGAGCTCTCTAGAGCCAAAGGACTCTGCACTGTTCTTCACAG
which has a whitespace between 289 and the sequence (the crash is in the parseInt at this line).
I haven't checked whether there are more lines with whitespace instead of tab. Instead of fixing all offending lines, it may be worth to change the splitEachLine
pattern to include all space-like characters, eg by using \s
.