Use buffer-size to limit CLI args for samtools/tabix

Author: ckandoth

vcf2maf.pl

@@ -359,11 +359,11 @@ sub GetBiotypePriority {
 $vcf_fh->close;
 
 # samtools runs faster when passed many loci at a time, but limited to around 125k args, at least
-# on CentOS 6. If there are too many loci, split them into 50k chunks and run separately
+# on CentOS 6. If there are too many loci, split them into smaller chunks and run separately
 my ( $lines, @regions_split ) = ( "", ());
 my @regions = keys %uniq_regions;
 my $chr_prefix_in_use = ( @regions and $regions[0] =~ m/^chr/ ? 1 : 0 );
-push( @regions_split, [ splice( @regions, 0, 50000 ) ] ) while @regions;
+push( @regions_split, [ splice( @regions, 0, $buffer_size ) ] ) while @regions;
 map{ my $region = join( " ", @{$_} ); $lines .= `$samtools faidx $ref_fasta $region` } @regions_split;
 foreach my $line ( grep( length, split( ">", $lines ))) {
     # Carefully split this FASTA entry, properly chomping newlines for long indels
@@ -386,7 +386,7 @@ sub GetBiotypePriority {
     # Query each variant locus on the filter VCF, using tabix, just like we used samtools earlier
     ( $lines, @regions_split ) = ( "", ());
     my @regions = keys %uniq_loci;
-    push( @regions_split, [ splice( @regions, 0, 50000 ) ] ) while @regions;
+    push( @regions_split, [ splice( @regions, 0, $buffer_size ) ] ) while @regions;
     # ::NOTE:: chr-prefix removal works safely here because ExAC is limited to 1..22, X, Y
     map{ my $loci = join( " ", map{s/^chr//; $_} @{$_} ); $lines .= `$tabix $filter_vcf $loci` } @regions_split;
     foreach my $line ( split( "\n", $lines )) {