Imported Upstream version 0.1.12a

[samtools.git] / bcftools / vcfutils.pl

diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl
index 6cc168fb363f59541511429b6e6538e0263acbe1..cd86b0fba041a77bb9d887473fa68cb853f1c597 100755 (executable)
--- a/bcftools/vcfutils.pl
+++ b/bcftools/vcfutils.pl
@@ -14,11 +14,27 @@ sub main {
   my $command = shift(@ARGV);
   my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
                          hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
-                         gapstats=>\&gapstats);
+                         gapstats=>\&gapstats, splitchr=>\&splitchr);
   die("Unknown command \"$command\".\n") if (!defined($func{$command}));
   &{$func{$command}};
 }
 
+sub splitchr {
+  my %opts = (l=>5000000);
+  getopts('l:', \%opts);
+  my $l = $opts{l};
+  die(qq/Usage: vcfutils.pl splitchr [-l $opts{l}] <in.fa.fai>\n/) if (@ARGV == 0 && -t STDIN);
+  while (<>) {
+       my @t = split;
+       my $last = 0;
+       for (my $i = 0; $i < $t[1];) {
+         my $e = ($t[1] - $i) / $l < 1.1? $t[1] : $i + $l;
+         print "$t[0]:".($i+1)."-$e\n";
+         $i = $e;
+       }
+  }
+}
+
 sub subsam {
   die(qq/Usage: vcfutils.pl subsam <in.vcf> [samples]\n/) if (@ARGV == 0);
   my ($fh, %h);