From cf7f9a21b8d639245c60da9f30745e4332e4d079 Mon Sep 17 00:00:00 2001 From: "Brankovics, Balazs" <balazs.brankovics@wur.nl> Date: Fri, 31 Mar 2023 14:07:44 +0200 Subject: [PATCH] bug fixed to allow AS:i:0 as valid score --- src/sam-keep-best.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sam-keep-best.pl b/src/sam-keep-best.pl index 199778f..1a353d3 100755 --- a/src/sam-keep-best.pl +++ b/src/sam-keep-best.pl @@ -422,7 +422,7 @@ sub update_pair { my %hit = %$hitref; if ($term eq 'AS:i') { - unless ($hit{'AS:i'}) { + unless (defined $hit{'AS:i'}) { # Make SAM output invalid to make the mistake obvious and die with error print "ERROR: Aborted, due to missing alignment score ('AS:i:<int>' column). Check STDERR for more info.\n"; die "ERROR: Hit does not have an alignment score ('AS:i:<int>' column).\n" . @@ -431,7 +431,7 @@ sub update_pair { } $pair->{$term} += $hit{$term}; } elsif ($term eq 'BS:f') { - unless ($hit{'BS:f'}) { + unless (defined $hit{'BS:f'}) { # Make SAM output invalid to make the mistake obvious and die with error print "ERROR: Aborted, due to missing bitscore ('BS:f:<num>' column). Check STDERR for more info.\n"; die "ERROR: Hit does not have a bitscore ('BS:f:<num>' column).\n" . -- GitLab