From c98347f145e9e938ca97fad69a1d1d3bd3e44bd2 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 4 Nov 2009 20:07:13 +0000
Subject: [PATCH] corrected ALIGN implementation

git-svn-id: http://biopieces.googlecode.com/svn/trunk@747 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/KISS/IO.pm | 38 +++++++++++--------------------------
 1 file changed, 11 insertions(+), 27 deletions(-)

diff --git a/code_perl/Maasha/KISS/IO.pm b/code_perl/Maasha/KISS/IO.pm
index a24f696..f7fa8d9 100644
--- a/code_perl/Maasha/KISS/IO.pm
+++ b/code_perl/Maasha/KISS/IO.pm
@@ -24,6 +24,8 @@ package Maasha::KISS::IO;
 
 # Routines for parsing and emitting KISS records.
 
+# http://code.google.com/p/biopieces/wiki/KissFormat
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -53,28 +55,6 @@ use constant {
     BLOCK_TYPE  => 11,
 };
 
-#      0         1         2
-#      012345678901234567890
-#      ---------------------   S.aur complete genome
-#         -===__===-           TAG_000001
-#         0123456789
-#
-#    S_ID        = 'S.aur complete genome'
-#    S_BEG       = 3
-#    S_END       = 12
-#    Q_ID        = 'TAG_000001'
-#    SCORE       => 1
-#    STRAND      => +
-#    HITS        => 31
-#    ALIGN       => 0:A>T,3:G>C
-#    BLOCK_COUNT => 2
-#    BLOCK_BEGS  => 1,6
-#    BLOCK_LENS  => 3,3
-#    BLOCK_TYPE  => 1,1
-#
-#
-# 'S.aur complete genome'   3   12  'TAG_000001'    1   +   31   2   1,6 3,3    1,1
-
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -309,11 +289,13 @@ sub kiss_align
 
     # Returns a string.
 
-    my ( $align, $pos, $s_symbol, $q_symbol, $s_seq, $q_seq );
+    my ( $align, $pos, $s_symbol, $q_symbol, $s_seq, $q_seq, $insertions );
 
     $s_seq = substr ${ $s_seqref }, $entry->{ 'S_BEG' }, $entry->{ 'S_END' } - $entry->{ 'S_BEG' } + 1;
     $q_seq = $s_seq;
 
+    $insertions = 0;
+
     foreach $align ( split /,/, $entry->{ 'ALIGN' } )
     {
         if ( $align =~ /(\d+):(.)>(.)/ )
@@ -324,16 +306,18 @@ sub kiss_align
 
             if ( $s_symbol eq '-' ) # insertion
             {
-                substr $s_seq, $pos, 0, $s_symbol;
-                substr $q_seq, $pos, 0, $q_symbol;
+                substr $s_seq, $pos + $insertions, 0, $s_symbol;
+                substr $q_seq, $pos + $insertions, 0, $q_symbol;
+
+                $insertions++;
             }
             elsif ( $q_symbol eq '-' ) # deletion
             {
-                substr $q_seq, $pos, 1, $q_symbol;
+                substr $q_seq, $pos + $insertions, 1, $q_symbol;
             }
             else # mismatch
             {
-                substr $q_seq, $pos, 1, $q_symbol;
+                substr $q_seq, $pos + $insertions, 1, $q_symbol;
             }
         }
         else
-- 
2.39.2