--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_bam_by_list	Wed Mar 25 13:33:46 2015 -0600
@@ -0,0 +1,55 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use IO::Handle;
+
+# Report lines of a file that have as one of the column values a value from the pattern file
+@ARGV == 6 or die "Usage: $0 <input.bam> <named genomic regions.bed> <file of patterns> <filtered output.bam> <matched regions.bed> <output messages.txt>\n";
+
+die "Input BAM file $ARGV[0] does not exist\n" if not -e $ARGV[0];
+die "Input BAM file $ARGV[0] is not readable\n" if not -r $ARGV[0];
+
+my @alts;
+if(-e $ARGV[2]){
+  open(PATTERNS, $ARGV[2])
+    or die "Cannot open $ARGV[1] for reading: $!\n";
+  while(<PATTERNS>){
+    chomp;
+    push @alts, $_;
+  }
+  close(PATTERNS);
+}
+else{ # else assume the arg is a list of names directly
+  @alts = split /\s+/, $ARGV[2];
+}
+
+my @regions;
+my %seen;
+my $regex = "^(?:".join("|", @alts).")\$";
+open(TAB, $ARGV[1])
+  or die "Cannot open $ARGV[1] for reading: $!\n";
+while(<TAB>){
+  chomp;
+  my @F = split /\t/, $_;
+  next unless @F > 3;
+  if($F[3] =~ /$regex/io){
+    next if $seen{"$F[0]:$F[1]-$F[2]"}++; # sometimes regions are repeated, don't send these repeats to samtools
+    push @regions, $_;
+  }
+}
+close(TAB);
+
+die "No matches to desired names in the provided named genomic regions BED file, aborting filtered BAM file creation" if not @regions;
+
+open(BED, ">$ARGV[4]")
+  or die "Cannot open $ARGV[4] for writing: $!\n";
+print BED join("\n", @regions), "\n";
+close(BED);
+
+open(ERRFILE, ">$ARGV[5]") or die "Cannot open $ARGV[5] for writing: $!\n";
+STDOUT->fdopen(\*ERRFILE, "w") or die "Cannot redirect stdout to $ARGV[5]: $!\n";
+STDERR->fdopen(\*ERRFILE, "w") or die "Cannot redirect stderr to $ARGV[5]: $!\n";
+system("samtools view -h -L $ARGV[4] $ARGV[0] | samtools view -S -b - > $ARGV[3]") >> 8 
+  and die "Samtools failed: exit status ", ($?>>8), "\n"; 
+system("samtools index $ARGV[3]");