The --gene-list option can be used for any field

Show that the -g and --gene-list-fields options can be used
for any field, not just a gene name

Author: pd3

plugins/split-vep.c

@@ -210,8 +210,8 @@ static const char *usage_text(void)
         "   -d, --duplicate                 Output per transcript/allele consequences on a new line rather rather than\n"
         "                                     as comma-separated fields on a single line\n"
         "   -f, --format STR                Create non-VCF output; similar to `bcftools query -f` but drops lines w/o consequence\n"
-        "   -g, --gene-list [+]FILE         Consider only genes listed in FILE, or prioritize if FILE is prefixed with \"+\"\n"
-        "       --gene-list-fields LIST     Use these fields when matching genes from the -g list [SYMBOL,Gene,gene]\n"
+        "   -g, --gene-list [+]FILE         Consider only features listed in FILE, or prioritize if FILE is prefixed with \"+\"\n"
+        "       --gene-list-fields LIST     Fields to match against by the -g list, by default gene names [SYMBOL,Gene,gene]\n"
         "   -H, --print-header              Print header\n"
         "   -l, --list                      Parse the VCF header and list the annotation fields\n"
         "   -p, --annot-prefix STR          Before doing anything else, prepend STR to all CSQ fields to avoid tag name conflicts\n"

test/split-vep.mixed-list.txt

@@ -0,0 +1,3 @@
+ENST00000344229
+ENST00000317578
+RPL10

test/test.pl

@@ -668,7 +668,9 @@
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.10',out=>'split-vep.25.out',cmd=>'+split-vep',args=>qq[-a CSQ -f '%xM_CAP_pred %xM_CAP_score\\n' -p x | grep -v ^#]);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.1.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n']);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g {PATH}/split-vep.gene-list.txt]);
+run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g {PATH}/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL]);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.3.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g +{PATH}/split-vep.gene-list.txt]);
+run_test(\&test_vcf_plugin,$opts,in=>'split-vep.gene-list',out=>'split-vep.gene-list.3.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Gene %Consequence\\n' -g +{PATH}/split-vep.mixed-list.txt --gene-list-fields Feature,SYMBOL]);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.broken-LoF',out=>'split-vep.broken-LoF.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %Consequence %LoF_info\\n' -a vep]);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep.broken-LoF',out=>'split-vep.broken-LoF.2.out',cmd=>'+split-vep',args=>qq[-d -f '%CHROM:%POS %LoF_info\\n' -a vep -i 'Consequence=="frameshift_variant"']);
 run_test(\&test_vcf_plugin,$opts,in=>'split-vep',out=>'split-vep.26.out',cmd=>'+split-vep',args=>qq[-f'%POS\\n' -i'SYMBOL~"SAMD11"']);