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Use tabix when splitting imputation server vcfs #60

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2 changes: 1 addition & 1 deletion rp_bin/Ricopili/Version.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ our ($rp_header, $rp_version);



$rp_version = "2019_Feb_18.001" ;
$rp_version = "2019_Feb_20.001" ;


my $rp_logo = <<'END_TXT';
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10 changes: 10 additions & 0 deletions rp_bin/impute_dirsub
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Expand Up @@ -3743,6 +3743,16 @@ if ($impdeploy_done == 0) {
exit;
}
}

# check for vcf index files (csi or tbi)
unless (-e "$vcf_file.csi" || -e "$vcf_file.tbi") {
print "------------------------------------------------------------------------------------------------------------\n";
print "Error: $vcf_file index (csi or tbi) not found\n";
print "Please copy from imputation server output or generate in $subdir_in with \"tabix -p vcf\"\n";
print "------------------------------------------------------------------------------------------------------------\n";
exit;
}

my $keep_txt = "";
$keep_txt = "--keepvcf" if ($noclean);

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19 changes: 16 additions & 3 deletions rp_bin/vcf2dos
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Expand Up @@ -15,6 +15,7 @@ use Ricopili::Utils qw(trans);

use lib $ENV{rp_perlpackages};
use Compress::Zlib ;
use IO::Zlib;
#use Time;


Expand Down Expand Up @@ -235,7 +236,18 @@ if ($legend_sw == 1) {
## translate vcf file
##############################################

my $igz = gzopen("$vcf_file", "rb") or die "Cannot open file $vcf_file: $gzerrno\n" ;
# check for vcf index file and use with tabix if present
# if not, read entire file as before
my $vcf_has_index = -e "$vcf_file.csi" || -e "$vcf_file.tbi";

if ($vcf_has_index) {
my $tabix = trans("tabixloc") . "/tabix";
my $tabix_cmd = "$tabix -h $vcf_file $chr:$start_loc-$end_loc";
die $!."$tabix_cmd" unless open VCF, "-|", "$tabix_cmd";
} else {
die $!."$vcf_file" unless tie *VCF, "IO::Zlib", "$vcf_file", "rb";
}

my $ovgz = gzopen("$outvcf", "wb") or die "Cannot open file $outvcf: $gzerrno\n" ;
my $odgz = gzopen("$outdos", "wb") or die "Cannot open file $outdos: $gzerrno\n" ;

Expand All @@ -248,7 +260,8 @@ die $!."$outmap" unless open MAP, "> $outmap";
print "translating $vcf_file into $outvcf and $outdos\n";

my $nwarnings=0;
while ($igz->gzreadline(my $line)){

while (my $line = <VCF>){
chomp($line);
my @cells = @{&split_line_ref_tab(\$line)};

Expand Down Expand Up @@ -383,7 +396,7 @@ while ($igz->gzreadline(my $line)){

}

$igz->gzclose();
close VCF;
$ovgz->gzclose();
$odgz->gzclose();
close MAP;
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