From f8915b79363e896409bd9ca56819f56c3f77a47e Mon Sep 17 00:00:00 2001
From: mourisl <mourisl@hotmail.com>
Date: Tue, 27 Feb 2024 13:53:09 -0500
Subject: [PATCH] Add the option to specify the directory for temporary files.

---
 README.md         |  1 +
 run_rcorrector.pl | 27 +++++++++++++++++----------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 6b0f99a..ad2f891 100644
--- a/README.md
+++ b/README.md
@@ -37,6 +37,7 @@ Rcorrector can also be applied to other type of sequencing data where the read c
 		-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
 		-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
 		-stdout: output the corrected reads to stdout (default: not used)
+		-tmpd temp_file_directory: directory for tempoary files (default: ./)
 		-verbose: output some correction information to stdout (default: not used)
 		-stage INT: start from which stage (default: 0)
 			0-start from begining(storing kmers in bloom filter) ;
diff --git a/run_rcorrector.pl b/run_rcorrector.pl
index ba7b85f..c913c5e 100644
--- a/run_rcorrector.pl
+++ b/run_rcorrector.pl
@@ -30,6 +30,7 @@
 		"\t-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)\n".
 		"\t-ek expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)\n".
 		"\t-stdout: output the corrected reads to stdout (default: not used)\n".
+		"\t-tmpd temp_file_directory: directory for tempoary files (default: ./)\n".
 		"\t-version: print the version information and quit\n".
 		"\t-verbose: output some correction information to stdout (default: not used)\n".
 		"\t-stage INT: start from which stage (default: 0)\n".
@@ -61,6 +62,7 @@
 
 my @rcorrectorArguments ;
 my @gzippedFileList ;
+my $tmpdir = "./" ;
 
 sub AddJellyFishReadFile
 {
@@ -197,6 +199,11 @@ sub AddJellyFishReadFile
 		push @rcorrectorArguments, $ARGV[$i + 1] ;
 		++$i ;
 	}
+	elsif ( $ARGV[$i] eq "-tmpd" )
+	{
+		$tmpdir = $ARGV[$i + 1] ;
+		++$i ;
+	}
 	elsif ( $ARGV[$i] eq "-wk" )
 	{
 		push @rcorrectorArguments, $ARGV[$i] ;
@@ -205,7 +212,7 @@ sub AddJellyFishReadFile
 	}
 	elsif ( $ARGV[$i] eq "-version" )
 	{
-		print ( "Rcorrector v1.0.5\n" ) ;
+		print ( "Rcorrector v1.0.7\n" ) ;
 		exit( 0 ) ;
 	}
 	else
@@ -255,29 +262,29 @@ sub AddJellyFishReadFile
 if ( $stage <= 0 )
 {
 	print STDERR ( "Put the kmers into bloom filter\n" ) ;
-	print STDERR ( "$jellyfishBin bc -m $kmerSize -s $bloomFilterSize -C -t $numOfThread -o tmp_$crc.bc $jellyfishFiles\n" ) ;
-	die "Failed at stage 0.\n" if ( system( "bash -c \"$jellyfishBin bc -m $kmerSize -s $bloomFilterSize -C -t $numOfThread -o tmp_$crc.bc $jellyfishFiles\"" ) != 0 ) ;
+	print STDERR ( "$jellyfishBin bc -m $kmerSize -s $bloomFilterSize -C -t $numOfThread -o $tmpdir/tmp_$crc.bc $jellyfishFiles\n" ) ;
+	die "Failed at stage 0.\n" if ( system( "bash -c \"$jellyfishBin bc -m $kmerSize -s $bloomFilterSize -C -t $numOfThread -o $tmpdir/tmp_$crc.bc $jellyfishFiles\"" ) != 0 ) ;
 }
 
 if ( $stage <= 1 )
 {
 	print STDERR ( "Count the kmers in the bloom filter\n" ) ;
-	print STDERR ( "$jellyfishBin count -m $kmerSize -s 100000 -C -t $numOfThread --bc tmp_$crc.bc -o tmp_$crc.mer_counts $jellyfishFiles\n" ) ;
-	die "Failed at stage 1.\n" if ( system( "bash -c \"$jellyfishBin count -m $kmerSize -s 100000 -C -t $numOfThread --bc tmp_$crc.bc -o tmp_$crc.mer_counts $jellyfishFiles\"" ) != 0 ) ;
+	print STDERR ( "$jellyfishBin count -m $kmerSize -s 100000 -C -t $numOfThread --bc $tmpdir/tmp_$crc.bc -o $tmpdir/tmp_$crc.mer_counts $jellyfishFiles\n" ) ;
+	die "Failed at stage 1.\n" if ( system( "bash -c \"$jellyfishBin count -m $kmerSize -s 100000 -C -t $numOfThread --bc $tmpdir/tmp_$crc.bc -o $tmpdir/tmp_$crc.mer_counts $jellyfishFiles\"" ) != 0 ) ;
 }
 
 if ( $stage <= 2 )
 {
 	print STDERR ( "Dump the kmers\n" ) ;
-	print STDERR ( "$jellyfishBin dump -L 2 tmp_$crc.mer_counts > tmp_$crc.jf_dump\n" ) ;
-	die "Failed at stage 2.\n" if ( system( "$jellyfishBin dump -L 2 tmp_$crc.mer_counts > tmp_$crc.jf_dump" ) != 0 )
+	print STDERR ( "$jellyfishBin dump -L 2 $tmpdir/tmp_$crc.mer_counts > $tmpdir/tmp_$crc.jf_dump\n" ) ;
+	die "Failed at stage 2.\n" if ( system( "$jellyfishBin dump -L 2 $tmpdir/tmp_$crc.mer_counts > $tmpdir/tmp_$crc.jf_dump" ) != 0 )
 }
 
 if ( $stage <= 3 )
 {
 	print STDERR ( "Error correction\n" ) ;
-	print STDERR ( "$WD/rcorrector @rcorrectorArguments $fileArguments -c tmp_$crc.jf_dump\n" ) ;
-	die "Failed at stage 3.\n" if ( system( "$WD/rcorrector @rcorrectorArguments $fileArguments -c tmp_$crc.jf_dump" ) != 0 ) ;
+	print STDERR ( "$WD/rcorrector @rcorrectorArguments $fileArguments -c $tmpdir/tmp_$crc.jf_dump\n" ) ;
+	die "Failed at stage 3.\n" if ( system( "$WD/rcorrector @rcorrectorArguments $fileArguments -c $tmpdir/tmp_$crc.jf_dump" ) != 0 ) ;
 }
 
-system( "rm tmp_$crc.bc tmp_$crc.mer_counts tmp_$crc.jf_dump" );
+system( "rm $tmpdir/tmp_$crc.bc $tmpdir/tmp_$crc.mer_counts $tmpdir/tmp_$crc.jf_dump" );