bio-bwa 0.2.0

data/ext/kstring.c

@@ -0,0 +1,35 @@
+#include <stdarg.h>
+#include <stdio.h>
+#include "kstring.h"
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+	va_list ap;
+	int l;
+	va_start(ap, fmt);
+	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+	va_end(ap);
+	if (l + 1 > s->m - s->l) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+		va_start(ap, fmt);
+		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+	}
+	va_end(ap);
+	s->l += l;
+	return l;
+}
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+	kstring_t *s;
+	s = (kstring_t*)calloc(1, sizeof(kstring_t));
+	ksprintf(s, "abcdefg: %d", 100);
+	printf("%s\n", s->s);
+	free(s);
+	return 0;
+}
+#endif

data/ext/kstring.h

@@ -0,0 +1,46 @@
+#ifndef KSTRING_H
+#define KSTRING_H
+
+#include <stdlib.h>
+#include <string.h>
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+	int l = strlen(p);
+	if (s->l + l + 1 >= s->m) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	strcpy(s->s + s->l, p);
+	s->l += l;
+	return l;
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+	if (s->l + 1 >= s->m) {
+		s->m = s->l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+	}
+	s->s[s->l++] = c;
+	s->s[s->l] = 0;
+	return c;
+}
+
+int ksprintf(kstring_t *s, const char *fmt, ...);
+
+#endif

data/ext/kvec.h

@@ -0,0 +1,90 @@
+/* The MIT License
+
+   Copyright (c) 2008, by Attractive Chaos <attractivechaos@aol.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  An example:
+
+#include "kvec.h"
+int main() {
+	kvec_t(int) array;
+	kv_init(array);
+	kv_push(int, array, 10); // append
+	kv_a(int, array, 20) = 5; // dynamic
+	kv_A(array, 20) = 4; // static
+	kv_destroy(array);
+	return 0;
+}
+*/
+
+/*
+  2008-09-22 (0.1.0):
+
+	* The initial version.
+
+*/
+
+#ifndef AC_KVEC_H
+#define AC_KVEC_H
+
+#include <stdlib.h>
+
+#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+
+#define kvec_t(type) struct { size_t n, m; type *a; }
+#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
+#define kv_destroy(v) free((v).a)
+#define kv_A(v, i) ((v).a[(i)])
+#define kv_pop(v) ((v).a[--(v).n])
+#define kv_size(v) ((v).n)
+#define kv_max(v) ((v).m)
+
+#define kv_resize(type, v, s)  ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
+
+#define kv_copy(type, v1, v0) do {							\
+		if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n);	\
+		(v1).n = (v0).n;									\
+		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n);		\
+	} while (0)												\
+
+#define kv_push(type, v, x) do {									\
+		if ((v).n == (v).m) {										\
+			(v).m = (v).m? (v).m<<1 : 2;							\
+			(v).a = (type*)realloc((v).a, sizeof(type) * (v).m);	\
+		}															\
+		(v).a[(v).n++] = (x);										\
+	} while (0)
+
+#define kv_pushp(type, v) (((v).n == (v).m)?							\
+						   ((v).m = ((v).m? (v).m<<1 : 2),				\
+							(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0)	\
+						   : 0), ((v).a + ((v).n++))
+
+#define kv_a(type, v, i) ((v).m <= (size_t)(i)?						\
+						  ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
+						   (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
+						  : (v).n <= (size_t)(i)? (v).n = (i)			\
+						  : 0), (v).a[(i)]
+
+#endif

data/ext/main.c

@@ -0,0 +1,63 @@
+#include <stdio.h>
+#include <string.h>
+#include "main.h"
+
+#ifndef PACKAGE_VERSION
+#define PACKAGE_VERSION "0.5.9-r16"
+#endif
+
+static int usage()
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
+	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+	fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
+	fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
+	fprintf(stderr, "Command: index         index sequences in the FASTA format\n");
+	fprintf(stderr, "         aln           gapped/ungapped alignment\n");
+	fprintf(stderr, "         samse         generate alignment (single ended)\n");
+	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
+	fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
+	fprintf(stderr, "\n");
+	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
+	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
+	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
+	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
+	fprintf(stderr, "         pac_rev       generate reverse PAC\n");
+	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
+	fprintf(stderr, "         pac2cspac     convert PAC to color-space PAC\n");
+	fprintf(stderr, "         stdsw         standard SW/NW alignment\n");
+	fprintf(stderr, "\n");
+	return 1;
+}
+
+void bwa_print_sam_PG()
+{
+	printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
+}
+
+int main(int argc, char *argv[])
+{
+	if (argc < 2) return usage();
+	if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1);
+	else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1);
+	else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1);
+	else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1);
+	else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1);
+	else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1);
+	else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	return 0;
+}

data/ext/main.h

@@ -0,0 +1,29 @@
+#ifndef BWA_MAIN_H
+#define BWA_MAIN_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	int bwa_fa2pac(int argc, char *argv[]);
+	int bwa_pac_rev(int argc, char *argv[]);
+	int bwa_pac2cspac(int argc, char *argv[]);
+	int bwa_pac2bwt(int argc, char *argv[]);
+	int bwa_bwtupdate(int argc, char *argv[]);
+	int bwa_bwt2sa(int argc, char *argv[]);
+	int bwa_index(int argc, char *argv[]);
+	int bwa_aln(int argc, char *argv[]);
+	int bwt_bwtgen_main(int argc, char *argv[]);
+
+	int bwa_sai2sam_se(int argc, char *argv[]);
+	int bwa_sai2sam_pe(int argc, char *argv[]);
+
+	int bwa_stdsw(int argc, char *argv[]);
+
+	int bwa_bwtsw2(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

data/ext/mkrf_conf.rb

@@ -0,0 +1,49 @@
+# create Rakefile for shared library compilation
+
+require File.join("..",File.dirname(__FILE__),"lib/bio/bwa/library")
+
+path = File.expand_path(File.dirname(__FILE__))
+
+ext = Bio::BWA::Library.lib_extension
+
+flags = ""
+case ext
+  when "so" then flags = "-shared -Wl,-soname,libbwa.so"
+  when "dylib" then flags = "-bundle -undefined dynamic_lookup -flat_namespace"
+end
+
+
+File.open(File.join(path,"Rakefile"),"w") do |rakefile|
+rakefile.write <<-RAKE
+require 'rake/clean'
+    
+source = %w(utils.c bwt.c bwtio.c bwtaln.c bwtgap.c is.c bntseq.c bwtmisc.c bwtindex.c stdaln.c simple_dp.c bwaseqio.c bwase.c bwape.c kstring.c cs2nt.c bwtsw2_core.c bwtsw2_main.c bwtsw2_aux.c bwt_lite.c bwtsw2_chain.c bamlite.c main.c)
+    
+CLEAN.include('*.o')
+CLEAN.include('bwt_gen/*.o')
+
+GEN = FileList['bwt_gen/*.c']
+OBJ_GEN = GEN.ext('o')
+SRC = FileList.new(source)
+OBJ_SRC = SRC.ext('o')    
+
+rule '.o' => '.c' do |t|
+  sh "gcc -c -g -Wall -O2 -DHAVE_PTHREAD "+t.source+" -o "+t.name
+end
+    
+task :compile_gen => OBJ_GEN do
+  sh "ar -cru bwt_gen/libbwtgen.a "+OBJ_GEN.join(" ")
+end
+    
+task :compile_lib => OBJ_SRC do
+  sh "gcc #{flags} "+OBJ_SRC.join(" ")+" -o libbwa.#{ext} -lm -lz -lpthread -Lbwt_gen -lbwtgen"
+end
+  
+task :default => [:compile_gen, :compile_lib, :clean]
+  
+RAKE
+  
+end
+  
+  
+

data/ext/qualfa2fq.pl

@@ -0,0 +1,27 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
+
+my ($fhs, $fhq, $q);
+open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
+open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
+
+$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
+while (<$fhs>) {
+  $q = <$fhq>;
+  print "\@$_";
+  $/ = ">";
+  $_ = <$fhs>; $q = <$fhq>;
+  chomp; chomp($q);
+  $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
+  print $_, "+\n";
+  for (my $i = 0; $i < length($q); $i += 60) {
+	print substr($q, $i, 60), "\n";
+  }
+  $/ = "\n";
+}
+
+close($fhs); close($fhq);

data/ext/simple_dp.c

@@ -0,0 +1,162 @@
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <string.h>
+#include <zlib.h>
+#include <stdint.h>
+#include "stdaln.h"
+#include "utils.h"
+
+#include "kseq.h"
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct {
+	int l;
+	unsigned char *s;
+	char *n;
+} seq1_t;
+
+typedef struct {
+	int n_seqs, m_seqs;
+	seq1_t *seqs;
+} seqs_t;
+
+unsigned char aln_rev_table[256] = {
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
+	'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
+	'N','t','v','g', 'h','N','N','c', 'd','N','N','m', 'N','k','N','N',
+	'N','N','y','s', 'a','N','b','w', 'x','r','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
+	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
+};
+
+static int g_is_global = 0, g_thres = 1, g_strand = 0, g_aa = 0;
+static AlnParam g_aln_param;
+
+static void revseq(int len, uint8_t *seq)
+{
+	int i;
+	for (i = 0; i < len>>1; ++i) {
+		uint8_t tmp = aln_rev_table[seq[len-1-i]];
+		seq[len-1-i] = aln_rev_table[seq[i]];
+		seq[i] = tmp;
+	}
+	if (len&1) seq[i] = aln_rev_table[seq[i]];
+}
+
+static seqs_t *load_seqs(const char *fn)
+{
+	seqs_t *s;
+	seq1_t *p;
+	gzFile fp;
+	int l;
+	kseq_t *seq;
+
+	fp = xzopen(fn, "r");
+	seq = kseq_init(fp);
+	s = (seqs_t*)calloc(1, sizeof(seqs_t));
+	s->m_seqs = 256;
+	s->seqs = (seq1_t*)calloc(s->m_seqs, sizeof(seq1_t));
+	while ((l = kseq_read(seq)) >= 0) {
+		if (s->n_seqs == s->m_seqs) {
+			s->m_seqs <<= 1;
+			s->seqs = (seq1_t*)realloc(s->seqs, s->m_seqs * sizeof(seq1_t));
+		}
+		p = s->seqs + (s->n_seqs++);
+		p->l = seq->seq.l;
+		p->s = (unsigned char*)malloc(p->l + 1);
+		memcpy(p->s, seq->seq.s, p->l);
+		p->s[p->l] = 0;
+		p->n = strdup((const char*)seq->name.s);
+	}
+	kseq_destroy(seq);
+	gzclose(fp);
+	fprintf(stderr, "[load_seqs] %d sequences are loaded.\n", s->n_seqs);
+	return s;
+}
+
+static void aln_1seq(const seqs_t *ss, const char *name, int l, const char *s, char strand)
+{
+	int i;
+	for (i = 0; i < ss->n_seqs; ++i) {
+		AlnAln *aa;
+		seq1_t *p = ss->seqs + i;
+		g_aln_param.band_width = l + p->l;
+		aa = aln_stdaln_aux(s, (const char*)p->s, &g_aln_param, g_is_global, g_thres, l, p->l);
+		if (aa->score >= g_thres || g_is_global) {
+			printf(">%s\t%d\t%d\t%s\t%c\t%d\t%d\t%d\t%d\t", p->n, aa->start1? aa->start1 : 1, aa->end1, name, strand,
+				   aa->start2? aa->start2 : 1, aa->end2, aa->score, aa->subo);
+			// NB: I put the short sequence as the first sequence in SW, an insertion to
+			// the reference becomes a deletion from the short sequence. Therefore, I use
+			// "MDI" here rather than "MID", and print ->out2 first rather than ->out1.
+			for (i = 0; i != aa->n_cigar; ++i)
+				printf("%d%c", aa->cigar32[i]>>4, "MDI"[aa->cigar32[i]&0xf]);
+			printf("\n%s\n%s\n%s\n", aa->out2, aa->outm, aa->out1);
+		}
+		aln_free_AlnAln(aa);
+	}
+}
+
+static void aln_seqs(const seqs_t *ss, const char *fn)
+{
+	gzFile fp;
+	kseq_t *seq;
+	int l;
+
+	fp = xzopen(fn, "r");
+	seq = kseq_init(fp);
+	while ((l = kseq_read(seq)) >= 0) {
+		if (g_strand&1) aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '+');
+		if (g_strand&2) {
+			revseq(l, (uint8_t*)seq->seq.s);
+			aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '-');
+		}
+	}
+	kseq_destroy(seq);
+	gzclose(fp);
+}
+
+int bwa_stdsw(int argc, char *argv[])
+{
+	int c;
+	seqs_t *ss;
+	optind = 1;
+	while ((c = getopt(argc, argv, "gT:frp")) >= 0) {
+		switch (c) {
+		case 'g': g_is_global = 1; break;
+		case 'T': g_thres = atoi(optarg); break;
+		case 'f': g_strand |= 1; break;
+		case 'r': g_strand |= 2; break;
+		case 'p': g_aa = 1; break;
+		}
+	}
+	if (g_strand == 0) g_strand = 3;
+	if (g_aa) g_strand = 1;
+	if (optind + 1 >= argc) {
+		fprintf(stderr, "\nUsage:   bwa stdsw [options] <seq1.long.fa> <seq2.short.fa>\n\n");
+		fprintf(stderr, "Options: -T INT    minimum score [%d]\n", g_thres);
+		fprintf(stderr, "         -p        protein alignment (suppressing -r)\n");
+		fprintf(stderr, "         -f        forward strand only\n");
+		fprintf(stderr, "         -r        reverse strand only\n");
+		fprintf(stderr, "         -g        global alignment\n\n");
+		fprintf(stderr, "Note: This program is specifically designed for alignment between multiple short\n");
+		fprintf(stderr, "      sequences and ONE long sequence. It outputs the suboptimal score on the long\n");
+		fprintf(stderr, "      sequence.\n\n");
+		return 1;
+	}
+	g_aln_param = g_aa? aln_param_aa2aa : aln_param_blast;
+	g_aln_param.gap_end = 0;
+	ss = load_seqs(argv[optind]);
+	aln_seqs(ss, argv[optind+1]);
+	return 0;
+}