Added a check for all input files being devoid of sequence.

hepcat72 · Aug 13, 2015 · 67b33d7 · 67b33d7
1 parent cab80e8
commit 67b33d7
Showing 1 changed file with 25 additions and 1 deletion.
diff --git a/src/mergeSeqs.pl b/src/mergeSeqs.pl
@@ -13,7  13,7 @@
 #Copyright 2014
 
 #These variables (in main) are used by getVersion() and usage()
-my $software_version_number = '2.16';
 my $software_version_number = '2.17';
 my $created_on_date         = '3/26/2014';
 
 ##
@@ -455,6  455,8 @@
 my $abund_parse_errs = {};
 my $diff_sizes       = 0;
 my $size_error_mode  = ($trim_size == 0 ? 1 : 0);
 my $got_something    = 0;
 my $got_anything     = 0;
 
 #foreach my $input_file_set (@$input_files)
 foreach my $set_num (0..$#$input_file_sets)
@@ -588,6  590,8 @@
 	my($def,$seq) = @$rec;
 	$seq = uc($seq);
 
 	$got_anything = 1;
 
 	my $id = '';
 	if($def =~ /\s*[\@\>]\s*(\S )/)
 	  {
@@ -687,6  691,8 @@
 	      }
 	  }
 
 	$got_something = 1;
 
 	#Warn about possibly erroneous duplicate records if they have the same
 	#ID, the sequence exists, and the abundance of one of the records is
 	#greater than 1
@@ -788,6  794,24 @@
     quit(8);
   }
 
 unless($got_something)
   {
     if($got_anything)
       {
 	error("No viable sequences were found in any of the input files.  ",
 	      "Please check to make sure your trim length (-b) is not too ",
 	      "long and that your deflines are parseable.");
 	quit(9);
       }
     else
       {
 	error("No viable sequences were found in any of the input files.  ",
 	      "Please check to make sure your file paths are correct and ",
 	      "that your input files have sequences in them.");
 	quit(10);
       }
   }
 
 if($isglobal)
   {
     foreach my $current_outfile (keys(%$abundance_hash))