biohazard 0.6.1 → 0.6.2

raw patch · 3 files changed

+82/−6 lines, 3 files

Files

• biohazard.cabal +3/−3
• src/Bio/Bam/Evan.hs +3/−3
• src/cbits/myers_align.h +76/−0

@@ -1,5 +1,5 @@ Name:                biohazard-Version:             0.6.1+Version:             0.6.2 Synopsis:            bioinformatics support library Description:         This is a collection of modules I separated from                      various bioinformatics tools.  The hope is to make@@ -37,7 +37,7 @@ source-repository this   type:     git   location: git://github.com/udo-stenzel/biohazard.git-  tag:      0.6.1+  tag:      0.6.2   Library@@ -102,7 +102,7 @@    Ghc-options:         -Wall -auto-all   Hs-source-dirs:      src-  Include-dirs:        src/cbits+  Install-Includes:    src/cbits/myers_align.h   C-sources:           src/cbits/myers_align.c   CC-options:          -fPIC 

@@ -1,10 +1,10 @@ {-# LANGUAGE OverloadedStrings #-}-module Bio.Bam.Evan where---- ^ This module contains stuff relating to conventions local to MPI+-- | This module contains stuff relating to conventions local to MPI -- EVAN.  The code is needed regularly, but it can be harmful when -- applied to BAM files that follow different conventions.  Most -- importantly, no program should call these functions by default.++module Bio.Bam.Evan where  import Bio.Bam.Header import Bio.Bam.Rec

@@ -0,0 +1,76 @@+#ifndef INCLUDED_MYERS_ALIGN+#define INCLUDED_MYERS_ALIGN++enum myers_align_mode { +	myers_align_globally = 0,+	myers_align_is_prefix = 1,+	myers_align_has_prefix = 2 } ;++//! \brief aligns two sequences in O(nd) time+//! This alignment algorithm following Eugene W. Myers: "An O(ND)+//! Difference Algorithm and Its Variations".+//! Both input sequences are ASCIIZ-encoded with IUPAC ambiguity codes.+//! By definition, if ambiguity codes overlap, that's a match, else a+//! mismatch.  Mismatches and gaps count a unit penalty.  If mode is+//! myers_align_globally, both sequences must align completely.  If mode+//! is myers_align_is_prefix, seq_a must align completely as prefix of+//! seq_b.  If mode is myers_align_has_prefix, seq_b must align+//! completely as prefix of seq_a.  +//!+//! Note that the calculation time is O(nd) where n is the length of the+//! best alignment and d the number of differences in it, memory+//! consumption is O(maxd^2).+//!+//! \param seq_a First input sequence.+//! \param mode How to align (i.e. what gaps to count).+//! \param seq_b Second input sequence.+//! \param maxd Maximum penalty to consider.+//! \param bt_a Space to backtrace seq_a into, must have room for+//!             (strlen(seq_a)+maxd+1) characters.+//! \param bt_b Space to backtrace seq_b into, must have room for+//!             (strlen(seq_b)+maxd+1) characters.+//! \return The actual edit distance or UINT_MAX if the edit distance+//!         would be greater than maxd.+//!+unsigned myers_diff(+        const char *seq_a, int len_a, enum myers_align_mode mode,+        const char* seq_b, int len_b, int maxd,+        char *bt_a, char *bt_b ) ;++//! \brief converts an IUPAC ambiguity code to a bitmap+//! Each base is represented by a bit, makes checking for matches+//! easier.+inline int char_to_bitmap( char x ) +{+    switch( x & ~32 )+    {+        case 'A': return 1 ;+        case 'C': return 2 ;+        case 'G': return 4 ;+        case 'T': return 8 ;+        case 'U': return 8 ;++        case 'S': return 6 ;+        case 'W': return 9 ;+        case 'R': return 5 ;+        case 'Y': return 10 ;+        case 'K': return 12 ;+        case 'M': return 3 ;++        case 'B': return 14 ;+        case 'D': return 13 ;+        case 'H': return 11 ;+        case 'V': return 7 ;++        case 'N': return 15 ;+        default: return 0 ;+    }+}++inline int compatible( char x, char y ) { return (char_to_bitmap(x) & char_to_bitmap(y)) != 0 ; }++inline int min( int a, int b ) { return a < b ? a : b ; }+inline int max( int a, int b ) { return a < b ? b : a ; }+inline int max3( int a, int b, int c ) { return a < b ? max( b, c ) : max( a, c ) ; }++#endif