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Added back missing tests.
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These were commented out during windows testing and forgotten about.
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@jkbonfield
jkbonfield committed May 8, 2017
1 parent 4e69ebf commit ca59971
Showing 1 changed file with 18 additions and 18 deletions.
36 changes: 18 additions & 18 deletions test/test.pl
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Expand Up @@ -202,7 +202,7 @@
test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref --no-version');
test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT --no-version',args=>'-- -t . -n 0');
test_vcf_plugin($opts,in=>'setGT',out=>'setGT.1.out',cmd=>'+setGT --no-version',args=>'-- -t q -n 0 -i \'GT~"." && FMT/DP=30 && GQ=150\'');
#test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version');
test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');
test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy --no-version',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
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test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150],test_list=>1);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.2.out',args=>q[-a DP,DV -r17:100-600]); # test files from samtools mpileup test suite
#test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-600 --gvcf 0,2,5]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -s ^HG00101,HG00102]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -S ^{PATH}/mplp.samples]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.9.out',args=>q[-t17:100-150 -S {PATH}/mplp.9.samples]);
#test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.10.out',args=>q[-t17:100-150 -G {PATH}/mplp.10.samples]);
#test_mpileup($opts,in=>[qw(3)],out=>'mpileup/mpileup.11.out',args=>q[]);
#test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-s HG00102]);
#test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-s ^HG99999]);
#test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-G {PATH}/mplp.11.rgs]);
#test_csq($opts,in=>'csq',out=>'csq.1.out',cmd=>'-f {PATH}/csq.fa -g {PATH}/csq.gff3');
#test_csq_real($opts,in=>'csq');
test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-600 --gvcf 0,2,5]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -s ^HG00101,HG00102]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -S ^{PATH}/mplp.samples]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.9.out',args=>q[-t17:100-150 -S {PATH}/mplp.9.samples]);
test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.10.out',args=>q[-t17:100-150 -G {PATH}/mplp.10.samples]);
test_mpileup($opts,in=>[qw(3)],out=>'mpileup/mpileup.11.out',args=>q[]);
test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-s HG00102]);
test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-s ^HG99999]);
test_mpileup($opts,in=>[qw(3 4)],out=>'mpileup/mpileup.11.out',args=>q[-G {PATH}/mplp.11.rgs]);
test_csq($opts,in=>'csq',out=>'csq.1.out',cmd=>'-f {PATH}/csq.fa -g {PATH}/csq.gff3');
test_csq_real($opts,in=>'csq');
print "\nNumber of tests:\n";
printf " total .. %d\n", $$opts{nok}+$$opts{nfailed};
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