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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Insert size must be an integer #81

Open dariober opened 6 years ago

dariober commented 6 years ago

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.

# 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
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 commented 6 years ago

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