revert fqfilter to remove PE bug

README.md

@@ -29,6 +29,8 @@ We provide a script to convert zUMIs output into loom file automatically based o
 zUMIs will try to automatically do this, otherwise convert zUMIs output to loom by simply running `Rscript rds2loom.R myRun.yaml`.
 
 ## Changelog
+10 July 2020: [zUMIs2.9.1](https://github.com/sdparekh/zUMIs/releases/tag/2.9.1): Revert changes from pull request #194 (commit  #ff7e879) that introduced a bug when using PE reads.
+
 05 July 2020: [zUMIs2.9.0 released](https://github.com/sdparekh/zUMIs/releases/tag/2.9.0): Speed up STAR read mapping by parallel instances if enough resources are available. Change the main zUMIs script to `zUMIs.sh`. Speed up and reduce clutter by loading reads from bam files using parallelised Rsamtools calls instead of printing temporary text files. Speed up counting by parallelising exon / intron / exon+intron counting as well as downsamplings. Speed up by parallelising creation of wide format count matrices. 
 
 23 June 2020: zUMIs2.8.3: Merged code contribution from @gringer: prevent errors by emitting SAM headers in chunked unmapped .bam file output of fqfilter. Changed call to STAR to prevent stalling of samtools pipe. 

distilReads.pm

@@ -27,10 +27,9 @@ sub makeFileHandles{
 
     $fh="file".$j;
 
-    if ( open $fhTmp, '<', $file ) {
-      $file_handles{ $fh }{"id"} = $file.":".$pat.":".$fpat.":".$cframe;
-      $file_handles{ $fh }{"handle"} = $fhTmp;
-      close $fhTmp;
+    if ( open $fh, '<', $file ) {
+      $file_handles{ $fh } = $file.":".$pat.":".$fpat.":".$cframe;
+      close $fh;
     }
     else {
       warn "couldn't open $file for reading: $!\n";
@@ -40,13 +39,9 @@ sub makeFileHandles{
 }
 
 sub checkPhred{
-  my ($bqseq) = @_;
-  @quals = map {$_} unpack "C*", $bqseq;
-  my $offset = 33;
-  if (grep {$_ > 74} @quals) {
-    $offset = 64;
-  }
-  return $offset;
+    @quals = map {$_} unpack "C*", $bqseq;
+    if(grep {$_ > 74} @quals){$offset=64;}else{$offset=33;}
+    return $offset;
 }
 
 sub correctFrameshift{