Merge pull request #78 from dufeiyu/bed_update

Minor updates for coverageBed and launcher.pl

Author: dufeiyu

accessory_files/MyeloseqHD.16462-1615924889.CoverageQC.hg38.bed

@@ -138,7 +138,7 @@ chr7	102227364	102227671	CUX1_exon_21	+	CUX1	307	ENSG00000257923	ENST00000292535
 chr7	102234049	102234242	CUX1_exon_22	+	CUX1	193	ENSG00000257923	ENST00000292535	102234051	102234240	3434	1145
 chr7	102239317	102239586	CUX1_exon_23	+	CUX1	269	ENSG00000257923	ENST00000292535	102239319	102239584	3623	1208
 chr7	102248409	102249043	CUX1_exon_24	+	CUX1	634	ENSG00000257923	ENST00000292535	102248411	102249042	3888	1296
-chr7	140753272	140753395	BRAF_exon_16	-	BRAF	123	ENSG00000157764	ENST00000644969	140753274	140753393	1862	621
+chr7	140753272	140753395	BRAF_exon_15	-	BRAF	123	ENSG00000157764	ENST00000646891	140753274	140753393	1742	581
 chr7	148807644	148807708	EZH2_exon_20	-	EZH2	64	ENSG00000106462	ENST00000320356	148807645	148807706	2196	732
 chr7	148809068	148809157	EZH2_exon_19	-	EZH2	89	ENSG00000106462	ENST00000320356	148809070	148809155	2111	704
 chr7	148809307	148809392	EZH2_exon_18	-	EZH2	85	ENSG00000106462	ENST00000320356	148809309	148809390	2030	677

scripts/launcher.pl

@@ -70,7 +70,14 @@
         die "Lane number is expected, Check sample sheet spreadsheet";
     }
     my ($lane, $flowcell, $lib, $index_str, $exception) = @$row;
-    $exception =~ s/\s+/_/g if $exception;
+
+    if ($exception) {
+        $exception =~ s/^\s+//;
+        $exception =~ s/\s+$//;
+        $exception =~ s/,\s+/,/g;
+        $exception =~ s/\s+,/,/g;
+        $exception =~ s/\s+/_/g;
+    }
 
     if ($exception and $exception =~ /NOTRANSFER/ and $exception =~ /RESEQ/) {
         die "$lib has both NOTRANSFER and RESEQ as exception and only one is allowed.";
@@ -81,7 +88,7 @@
     #my $id = $lib =~ /^H_|Research/ ? 'NONE' : $mrn.'_'.$accession;
     my $id = ($exception and $exception =~ /RESEQ|RESEARCH|NOTRANSFER/) ? 'NONE' : $mrn.'_'.$accession;
 
-    ($sample) = $lib =~ /^(\S+)\-lib/ if $lib =~ /^H_|Research/;
+    ($sample) = $lib =~ /^(\S+)\-lib/ if $lib =~ /^H_|Research|Positive\-Control/;
 
     unless ($id eq 'NONE') {
         unless ($mrn and $accession) {