20251125

99.scripts/trinity_utils/util/misc/hicpipe_raw_converter.pl

@@ -0,0 +1,23 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "usage: $0  bowtie.raw  \n\n";
+
+my $bowtie_raw = $ARGV[0] or die $usage;
+
+open (my $fh, $bowtie_raw) or die "Error, cannot open file $bowtie_raw";
+
+my $header = <$fh>;
+print $header;
+
+while (<$fh>) {
+    if (/random/) { next; }
+    if (/chrUn/) { next; }
+    s/chr//g;
+    print;
+}
+
+exit(0);
+