v0.1c

itmat · Mar 7, 2017 · cb187ed · cb187ed
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commit cb187ed
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diff --git a/README.md b/README.md
@@ -17,5 +17,5 @@
 
 ### Requirements
 * bowtie2-2.2.9: Download bowtie2-2.2.9 from [here.](https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9)
-* RAM: 2G per fastq/fasta file. 
+* RAM: 2.5G per fastq/fasta file. 
 
diff --git a/scripts/search1.pl b/scripts/search1.pl
@@ -75,71 +75,6 @@
 	}
 	$di_ct++;
     }
-=comment
-    #check which comes first I or D.
-    my $first = "";
-    foreach my $char (split //, $cig) {
-	if ($char eq 'I'){
-	    $first = "I";
-	    last;
-	}
-	if ($char eq 'D'){
-	    $first = "D";
-	    last;
-	}
-    }
-    my (%DP,%IP);
-    my $d_ct = 1;
-    my $i_ct = 1;
-    if ($first eq "D"){
-	while ($cig =~ /(\d+)M(\d+)D(\d+)M/){
-	    my $N = $1+$2+$3;
-	    my $str = $1 . "M" . $2 . "D" . $3 . "M";
-	    my $dpos = $1;
-	    my $dcnt = $2;
-#	    print "dpos:$dpos\tdcnt:$dcnt\n";
-	    $DP{"$d_ct.$dpos"} = "$dcnt";
-	    my $new_str = $N . "M";
-	    $cig =~ s/$str/$new_str/;
-	    $d_ct++;
-	}
-	while ($cig =~ /(\d+)M(\d+)I(\d+)M/){ #insertion
-#	    my $N = $1+$2+$3;
-	    my $N = $1+$3;
-	    my $str = $1 . "M" . $2 . "I" . $3 . "M";
-	    my $Icnt = $2;
-	    my $Ipos = $1;
-	    $IP{"$i_ct.$Ipos"} = "$Icnt";
-	    my $new_str = $N . "M";
-	    $cig =~ s/$str/$new_str/;
-	    $i_ct++;
-	}
-    }
-    else{
-	while ($cig =~ /(\d+)M(\d+)I(\d+)M/){ #insertion
-#            my $N = $1+$2+$3;
-            my $N = $1+$3;
-            my $str = $1 . "M" . $2 . "I" . $3 . "M";
-            my $Icnt = $2;
-            my $Ipos = $1;
-            $IP{"$i_ct.$Ipos"} = "$Icnt";
-            my $new_str = $N . "M";
-            $cig =~ s/$str/$new_str/;
-	    $i_ct++;
-        }
-	while ($cig =~ /(\d+)M(\d+)D(\d+)M/){
-            my $N = $1+$2+$3;
-            my $str = $1 . "M" . $2 . "D" . $3 . "M";
-            my $dpos = $1;
-            my $dcnt = $2;
-#            print "dpos:$dpos\tdcnt:$dcnt\n";
-            $DP{"$d_ct.$dpos"} = "$dcnt";
-            my $new_str = $N . "M";
-            $cig =~ s/$str/$new_str/;
-            $d_ct++;
-	}
-    }
-=cut
     $cig =~ /[^M\d]*(\d+)M/;
     my $M = $1;
     my $A = $sizeA - $N;