On Wed, Dec 14, 2016 at 08:00:00PM +0100, gregor herrmann wrote: > On Wed, 14 Dec 2016 08:58:30 +0100, Andreas Tille wrote: > > > On Tue, Nov 01, 2016 at 11:05:02AM +0000, Iain Lane wrote: > > > I noticed in Ubuntu, where we run autopkgtests as part of britney > > > migration, that vcftools fails now. You can see on ci.debian.net[0] > > > > > > > not ok 26 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../. > > > > -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt > > > > 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n' > > > > # Failed test 'Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl > > > > -I../. -MVcf /usr/bin/vcf-fix-ploidy -s fix-ploidy.samples -p > > > > fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n'' > > > > # at ./test.t line 452. > > > > # Structures begin differing at: > > > > # $got->[0] = '61098 M1 0/1 0,9,72,5,6,7 M2 0/0 > > > > 0,15,140,5,6,7 F3 1 147,0,5 F4 0 0,131,5 M5 0/0 0,9,83,5,6,7 > > > > M6 0/0 0,6,56,5,6,7 > > > > # ' > > > > # $expected->[0] = '61098 M1 0 0,9,72,5,6,7 M2 0 > > > > 0,15,140,5,6,7 F3 1/1 147,0,5 F4 0/0 0,131,5 M5 0 0,9,83,5,6,7 > > > > M6 0 0,6,56,5,6,7 > > > > # '
> The tests started failing on 2016-09-01. > perl 5.24 entered unstable on 23 Sep 2016. > > What did happen around the time was the removal of '.' from @INC. That's indeed what caused the regression. > The test call can be shortened to: > > # vcf-fix-ploidy -s fix-ploidy.samples < fix-ploidy.vcf | grep 61098 > 20 61098 . C A,T 999 PASS > AC1=41;AF1=0.2104;DP4=209,284,67,76;DP=658;FQ=999;MQ=45;PV4=0.39,4.4e-10,0.0034,0.2 > GT:PL:DP:SP:GQ 0/1:0,9,72,5,6,7:3:212:12 0/0:0,15,140,5,6,7:5:458752:18 > 1:147,0,5:7:384:24 0:0,131,5:5:208:18 0/0:0,9,83,5,6,7:3:392:12 > 0/0:0,6,56,5,6,7:2:204:9 > > Which already has the 0/1:0,9,72,5,6,7 sequence which is not the > expected "0 0,9,72,5,6,7". And I don't know what either of them mean You missed the '-p' parameter above, which makes all the difference. It's loading Perl code from the specified file with 'do', which no longer looks in cwd. The load fails silently and the program continues on with wrong results. Patch attached. -- Niko Tyni nt...@debian.org
>From 8435d883d7d514618c8dcd8b60a722e163a261f6 Mon Sep 17 00:00:00 2001 From: Niko Tyni <nt...@debian.org> Date: Thu, 15 Dec 2016 01:39:16 +0200 Subject: [PATCH] vcf-fix-ploidy: make -p work without . on @INC 'do $file' only looks in @INC for unqualified file names, so prefix those with './' in case '.' is not on @INC. While at it, add diagnostics if sourcing the file fails altogether. Bug-Debian: https://bugs.debian.org/842794 --- src/perl/vcf-fix-ploidy | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/perl/vcf-fix-ploidy b/src/perl/vcf-fix-ploidy index 4fd380d..0140a21 100644 --- a/src/perl/vcf-fix-ploidy +++ b/src/perl/vcf-fix-ploidy @@ -75,7 +75,17 @@ sub parse_params }; while (defined(my $arg=shift(@ARGV))) { - if ( $arg eq '-p' || $arg eq '--ploidy' ) { my $file=shift(@ARGV); my $x=do $file; $$opts{ploidy}=$x; next } + if ( $arg eq '-p' || $arg eq '--ploidy' ) { + my $file=shift(@ARGV); + $file = "./$file" if $file !~ m{^/}; + my $x=do $file; + if (!defined $x) { + error("problem parsing \"$file\": $@") if $@; + error("problem doing \"$file\": $!"); + } + $$opts{ploidy}=$x; + next + } if ( $arg eq '-s' || $arg eq '--samples' ) { $$opts{samples}=shift(@ARGV); next } if ( $arg eq '-a' || $arg eq '--assumed-sex' ) { $$opts{assumed_sex}=shift(@ARGV); next } if ( $arg eq '-l' || $arg eq '--fix-likelihoods' ) { $$opts{fix_likelihoods}=1; next } -- 2.10.2
