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Resolved #28 #39

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creggian wants to merge 1 commit into molgenis:master from creggian:issue-28

creggian commented Jan 17, 2019

I got the same error when the BAM file had zero coverage in al least one (but not all) regions described in the BED file.

I solved by editing the samtools command by providing an additional "-a" option

my $extractcov = "samtools depth -r $chr:$start-$stop -a -a -q 0 -Q 0 $bam | awk '{sum+=$3} END {if (NR > 0) print sum/NR; else print 0;}'";

(see the my edit "-a" after the first "-a")

In this way samtools produces the expected output with 0 coverage in every position.

Versions

samtools v1.8 using htslib v1.8
CoNVaDING 1.2.1


          Fix molgenis#28

e590a46

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