difference on code to get working in our reads.

diff_nextgen_missmatch_qc.pl

2,3c2
< use lib '/scratch/lpantano/montreal/qc';
< use IO::Uncompress::Gunzip qw($GunzipError);
---
> use lib '/home/lpantano/soft/QC';
236c235
<         $INSTREAM = IO::Uncompress::Gunzip->new("$infile1") or die "Couldn't open $infile1\n";
---
>         open (INSTREAM, "$infile1") or die "Couldn't open $infile1\n";
239c238
<         while ($current_line = <$INSTREAM>) {
---
>         while ($current_line = <INSTREAM>) {
243,244d241
< 			$current_line =~ s/:/_/;
< 			$current_line =~ s/:/_/;
254c251
<         close $INSTREAM;
---
>         close INSTREAM;
257,258c254
<         #open (INSTREAM, "$infile2") or die "Couldn't open $infile2\n";
<         $INSTREAM = IO::Uncompress::Gunzip->new("$infile2") or die "Couldn't open $infile2\n";
---
>         open (INSTREAM, "$infile2") or die "Couldn't open $infile2\n";
261c257
<         while ($current_line = <$INSTREAM>) {
---
>         while ($current_line = <INSTREAM>) {
265,266d260
< 			$current_line =~ s/:/_/;
< 			$current_line =~ s/:/_/;
276c270
<         close $INSTREAM;
---
>         close INSTREAM;
280c274
< 	system ("bwa mem $ref -t 8 -c 1 Read1.fq Read2.fq >phix.sam");
---
> 	system ("bwa mem $ref -c 1 Read1.fq Read2.fq >phix.sam");
438,440c432
< 			@s=split(/\t/, $current_line);
<         		if ($s[5]=~/^\d+M$/) {
<         		#if ($current_line=~/80M/) {
---
>         		if ($current_line=~/80M/) {
467,469c459
< 			@s=split(/\t/, $current_line);
<         		if ($s[5]=~/^\d+M$/) {
<         		#if ($current_line=~/80M/) {
---
>         		if ($current_line=~/80M/) {
529,531c519
< 			@s=split(/\t/, $current_line);
<         		if ($s[5]=~/^\d+M$/) {
<         		#if ($current_line=~/80M/) {
---
>         		if ($current_line=~/80M/) {
558,559c546
< 			@s=split(/\t/, $current_line);
<         		if ($s[5]=~/^\d+M$/) {
---
>         		if ($current_line=~/80M/) {

original_reads

@NS500227:6:H160HBGXX:1:11101:12956:1048 1:N:0:1
AGTCANCACGCCCAGCCTAATCCTGAGATCTTGTAANACATCTGGNGAGCCAGGTGGCNTNACCNNTG
+
AAAA.#F<FFFFFAFFFAFAFFFFF<FFFAFFFFA.#FF<FFFFF#F<FF<FFF<FFF#F#FFF##F.
@NS500227:6:H160HBGXX:1:11101:21174:1048 1:N:0:1
TAACCNTCTTAACAGCCCTNGGACGGAGGAGTTACGNGTTTATCANCTCGGCTCTAAGNTNCAGNNA
+

Read1.fq

@NS500227_6_H160HBGXX:1:11108:2429:1048 1:N:0:1
AAAACNAAAAATGAGNTTAAATAACTANTNATATGNNTGTTATTTNCTGTNACTANNANANCTG
+
AA7AA#FF.FFF7FF#FFFF7FF<FAA#F#AFAFF##FF<<FA.F#7FF.#.F)<##<#.#FAF
@NS500227_6_H160HBGXX:1:11108:1920:1048 1:N:0:1
GAAGANGGTTCTGAGNATGCTTCTGATNTNGATCTNNGCGGTTTANCCCGNTAACNNCN
+