quick and dirty prinseq-lite.pl (versions 0.20.3/0.20.4) patch to enable mkfifo named pipes as input files; beware, this patch disables input file format checking

prinseq-lite.pl.patch

diff --git a/prinseq-lite.pl b/prinseq-lite.pl
index cad531a..de1eff3 100755
--- a/prinseq-lite.pl
+++ b/prinseq-lite.pl
@@ -583,7 +583,7 @@ if(exists $params{fasta} && exists $params{fastq}) {
         }
     } elsif(-e $params{fasta}) {
         #check for file format
-        my $format = &checkFileFormat($file1);
+        my $format = &checkFileFormat($file1, 'fasta');
         unless($format eq 'fasta') {
             &printError('input file for -fasta is in '.uc($format).' format not in FASTA format');
         }
@@ -600,7 +600,7 @@ if(exists $params{fasta} && exists $params{fastq}) {
         }
     } elsif(-e $params{fastq}) {
         #check for file format
-        my $format = &checkFileFormat($file1);
+        my $format = &checkFileFormat($file1, 'fastq');
         unless($format eq 'fastq') {
             &printError('input file for -fastq is in '.uc($format).' format not in FASTQ format');
         }
@@ -618,7 +618,7 @@ if(exists $params{fastq} && exists $params{qual}) {
         &printError('QUAL data cannot be read from STDIN');
     } elsif(-e $params{qual}) {
         #check for file format
-        my $format = &checkFileFormat($params{qual});
+        my $format = &checkFileFormat($params{qual}, 'qual');
         unless($format eq 'qual') {
             &printError('input file for -qual is in '.uc($format).' format not in QUAL format');
         }
@@ -640,7 +640,7 @@ if(exists $params{fasta2} && exists $params{fastq2}) {
             &printError('paired-end data cannot be processed from STDIN');
         } elsif(-e $params{fasta2}) {
             #check for file format
-            my $format = &checkFileFormat($file2);
+            my $format = &checkFileFormat($file2, 'fasta');
             unless($format eq 'fasta') {
                 &printError('input file for -fasta2 is in '.uc($format).' format not in FASTA format');
             }
@@ -661,7 +661,7 @@ if(exists $params{fasta2} && exists $params{fastq2}) {
             &printError('paired-end data cannot be processed from STDIN');
         } elsif(-e $params{fastq2}) {
             #check for file format
-            my $format = &checkFileFormat($file2);
+            my $format = &checkFileFormat($file2, 'fastq');
             unless($format eq 'fastq') {
                 &printError('input file for -fastq2 is in '.uc($format).' format not in FASTQ format');
             }
@@ -2370,6 +2370,17 @@ sub readParamsFile {
 
 sub checkFileFormat {
     my $file = shift;
+    # The proper FIFO fix would be:
+    # - only open file once, and close it also once - after processing is done;
+    # - if necessary - pass the file handle around;
+    # - for format checking, use the same method as for STDIN processing, namely
+    #   - read the first 3 lines into a variable;
+    #   - check format of those 3 lines;
+    #   - if the format is correct, then first process those lines from the variable,
+    #     and keep reading the file from line 4.
+    my $expected = shift;
+    # To (temporarily) undo the FIFO patch: comment out the return statement below.
+    return $expected;
 
     my ($format,$count,$id,$fasta,$fastq,$qual);
     $count = 3;