From 0253e2b8737fba111f4ec7406704dacaa4877d8d Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 25 Nov 2013 20:49:29 +0000
Subject: [PATCH] fixed encoding bug in read_454

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2257 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/read_454           |  2 +-
 bp_test/test_all          |  2 ++
 code_perl/Maasha/Fastq.pm | 17 +++++++++++++++++
 3 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/bp_bin/read_454 b/bp_bin/read_454
index 5017cd8..96c6a4f 100755
--- a/bp_bin/read_454
+++ b/bp_bin/read_454
@@ -130,7 +130,7 @@ sub get_qual
     $qual =~ tr/ \n\r/;;;/;
     $qual =~ s/;;/;/g;
 
-    $scores = Maasha::Fastq::dec_str2solexa_str( $qual );
+    $scores = Maasha::Fastq::dec_str2phred_str( $qual );
 
     $entry = [ $name, $scores ];
 
diff --git a/bp_test/test_all b/bp_test/test_all
index e94395f..fd358e7 100755
--- a/bp_test/test_all
+++ b/bp_test/test_all
@@ -21,7 +21,9 @@ test_aux_program "blastall"
 test_aux_program "blat"
 test_aux_program "bwa"
 test_aux_program "bowtie"
+test_aux_program "bowtie2"
 test_aux_program "formatdb"
+test_aux_program "hmmsearch"
 test_aux_program "gnuplot"
 test_aux_program "idba"
 test_aux_program "muscle"
diff --git a/code_perl/Maasha/Fastq.pm b/code_perl/Maasha/Fastq.pm
index b48279c..d70bf3e 100644
--- a/code_perl/Maasha/Fastq.pm
+++ b/code_perl/Maasha/Fastq.pm
@@ -443,6 +443,23 @@ sub dec_str2solexa_str
     return $scores;
 }
 
+sub dec_str2phred_str
+{
+    # Martin A. Hansen, November 2013.
+
+    # Converts a ; separated string of decimal scores to a
+    # string of Phred scores.
+
+    my ( $scores,   # Decimal score string
+       ) = @_;
+
+    # Returns a string.
+
+    $scores =~ s/(-\d{1,2})/0/g;
+    $scores =~ s/(\d{1,2});?/dec2phred( $1 )/eg;
+
+    return $scores;
+}
 
 sub get_entry
 {
-- 
2.39.2