#!/usr/bin/perl

# Tninsert_only_sam.pl
# By Kathryn Ramsey (ramsey.kathryn.m@gmail.com)
# Simon L. Dove Lab, Children's Hospital Boston, Harvard Medical School
# March 21, 2018

use strict;
use warnings;

my ($samfile, $outfile);
$samfile = shift @ARGV;
  unless ($samfile =~ /\.sam$/) {die "Tninsert_only_sam.pl - INPUT ERROR!\n";}

if ($samfile =~ /([0-9a-zA-Z_]*).sam/) { $outfile = $1."_TnOnly.sam"; }
else { die "Error! I didn't recognize the input well enough to define an output file name. Oops!\n";}

open SAM, $samfile or die "Could not open '$samfile': $!\n";
open OUT, ">$outfile" or die "Could not open $outfile': $!\n";

my ($line, @line);
my $count = 0;

while (<SAM>) {
  chomp;
  $line = $_;
  $count++;
  if ($count <= 3) {
    print OUT "$line\n";
  }
  else {
    @line = split;
    if ($line[1] == '0') {
      if ($line[9] =~ /TA$/) {
	print OUT "$line\n";
      }
    }
    if ($line[1] == '16') {
      if ($line[9] =~ /^TA/) {
	print OUT "$line\n";
      }
    }
  }
}
close SAM; close OUT;