Insert size must be an integer

[dariober]

Hello- It appears that average insert size in the config file must be an integer. If the insert size number contains a fractional part, the fractional part becomes the sample name in the output files.

The examples below should reproduce the bug (Pindel version 0.2.5b8, 20151210). Test files are from the pindel repository.

• This is ok:

# Prepare config
echo -e "test/SmallTest/sim1chrVs2.bam 123 my_sample" | tr ' ' '\t' > pindel.conf

pindel --fasta test/SmallTest/sim1chrVs2.fa \
       --config-file pindel.conf \
       --output-prefix my_test

head -n 2 my_test_D
###...
0   D 98    ...  NumSupSamples 1 1   my_sample 392 12 2 2 0 0

• Now use 123.4 as insert size:

echo -e "test/SmallTest/sim1chrVs2.bam 123.4 my_sample" | tr ' ' '\t' > pindel.conf

pindel --fasta test/SmallTest/sim1chrVs2.fa \
       --config-file pindel.conf \
       --output-prefix my_test

head -n 2 my_test_D
###...
0   D 98    ...   NumSupSamples 1 1   .4 392 12 2 2 0 0
                                      ^^^

[joelmartin]

was wondering where those decimals came from, that pull request fixes the parsing.