# HG changeset patch
# User romaingred
# Date 1510223330 18000
# Node ID 0a47c6cf912dc2383f8fd177b96d8161fc848af1
# Parent  aea6ed0da85baeb02cc96bc992996a44278adeae
Uploaded

diff -r aea6ed0da85b -r 0a47c6cf912d bin/piPipe.pl
--- a/bin/piPipe.pl	Tue Oct 24 05:23:42 2017 -0400
+++ b/bin/piPipe.pl	Thu Nov 09 05:28:50 2017 -0500
@@ -16,7 +16,7 @@
 use html qw ( main_page details_pages menu_page ppp_page );
 use File::Copy;
 
-my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $Dcheck, $mapnumf, $html_out);
+my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out);
 my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE );
 my ( $si_min, $si_max, $pi_min, $pi_max );
 my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_exons, $build_TE );
@@ -40,7 +40,6 @@
 	"misTE:i" => \$misTE,
 	"html:s" => \$html_out,
 	"PPPon:s" => \$Pcheck,
-	"Dison:s" => \$Dcheck,
 	"help"   =>  \$help,
 	"ref:s" => \$ref,
 	"tRNAs:s" => \$tRNAs,
@@ -213,8 +212,8 @@
 		my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt';
 		my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt';
 		rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo );
-		rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo );
-		rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo );
+		rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo );
+		rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo );
 
 		sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child );
 		sam_sorted_bam ( $type_sam_exons, $grand_child ); sam_sorted_bam ( $type_sam_uni_exons, $grand_child ); 
@@ -237,7 +236,7 @@
 
 		#HTML Details
 		my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child];
-		details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir );
+		details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck );
 
 		$pm2->finish();
 	}