Added an option to accept Illumina 1.3+ fastq

bwape.c

@@ -645,7 +645,7 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
 void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
-	int i, j, n_seqs, tot_seqs = 0;
+	int i, j, n_seqs, tot_seqs = 0, read_flag = 0;
 	bwa_seq_t *seqs[2];
 	bwa_seqio_t *ks[2];
 	clock_t t;
@@ -691,12 +691,14 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 	// core loop
 	bwa_print_sam_SQ(bns);
 	bwa_print_sam_PG();
-	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
+	read_flag |= (opt.mode & BWA_MODE_COMPREAD)? 1 : 0;
+	read_flag |= ((opt.mode & BWA_MODE_IL13)? 1 : 0)<<1;
+	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, read_flag, opt.trim_qual)) != 0) {
 		int cnt_chg;
 		isize_info_t ii;
 		ubyte_t *pacseq;
 
-		seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual);
+		seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, read_flag, opt.trim_qual);
 		tot_seqs += n_seqs;
 		t = clock();
 

bwase.c

@@ -587,7 +587,7 @@ int bwa_set_rg(const char *s)
 void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
-	int i, n_seqs, tot_seqs = 0, m_aln;
+	int i, n_seqs, tot_seqs = 0, m_aln, read_flag = 0;
 	bwt_aln1_t *aln = 0;
 	bwa_seq_t *seqs;
 	bwa_seqio_t *ks;
@@ -611,7 +611,9 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 	// set ks
 	ks = bwa_open_reads(opt.mode, fn_fa);
 	// core loop
-	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode & BWA_MODE_COMPREAD, opt.trim_qual)) != 0) {
+	read_flag |= (opt.mode & BWA_MODE_COMPREAD)? 1 : 0;
+	read_flag |= ((opt.mode & BWA_MODE_IL13)? 1 : 0)<<1;
+	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, read_flag, opt.trim_qual)) != 0) {
 		tot_seqs += n_seqs;
 		t = clock();
 

bwaseqio.c

@@ -139,17 +139,19 @@ static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_com
 	return seqs;
 }
 
- bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
+bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int flag, int trim_qual)
 {
 	bwa_seq_t *seqs, *p;
 	kseq_t *seq = bs->ks;
-	int n_seqs, l, i;
+	int n_seqs, l, i, is_comp = flag&1, is_64 = flag&2;
 	long n_trimmed = 0, n_tot = 0;
 
 	if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual);
 	n_seqs = 0;
 	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
 	while ((l = kseq_read(seq)) >= 0) {
+		if (is_64 && seq->qual.l)
+			for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
 		p = &seqs[n_seqs++];
 		p->tid = -1; // no assigned to a thread
 		p->qual = 0;

bwtaln.c

@@ -172,7 +172,7 @@ bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
 
 void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 {
-	int i, n_seqs, tot_seqs = 0;
+	int i, n_seqs, tot_seqs = 0, read_flag = 0;
 	bwa_seq_t *seqs;
 	bwa_seqio_t *ks;
 	clock_t t;
@@ -190,7 +190,9 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 
 	// core loop
 	fwrite(opt, sizeof(gap_opt_t), 1, stdout);
-	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode & BWA_MODE_COMPREAD, opt->trim_qual)) != 0) {
+	read_flag |= (opt->mode & BWA_MODE_COMPREAD)? 1 : 0;
+	read_flag |= ((opt->mode & BWA_MODE_IL13)? 1 : 0)<<1;
+	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, read_flag, opt->trim_qual)) != 0) {
 		tot_seqs += n_seqs;
 		t = clock();
 
@@ -246,7 +248,7 @@ int bwa_aln(int argc, char *argv[])
 	gap_opt_t *opt;
 
 	opt = gap_init_opt();
-	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012")) >= 0) {
+	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:b012I")) >= 0) {
 		switch (c) {
 		case 'n':
 			if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
@@ -273,6 +275,7 @@ int bwa_aln(int argc, char *argv[])
 		case '0': opt->mode |= BWA_MODE_BAM_SE; break;
 		case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
 		case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
+		case 'I': opt->mode |= BWA_MODE_IL13; break;
 		default: return 1;
 		}
 	}
@@ -303,6 +306,7 @@ int bwa_aln(int argc, char *argv[])
 		fprintf(stderr, "         -c        input sequences are in the color space\n");
 		fprintf(stderr, "         -L        log-scaled gap penalty for long deletions\n");
 		fprintf(stderr, "         -N        non-iterative mode: search for all n-difference hits (slooow)\n");
+		fprintf(stderr, "         -I        the input is in the Illumina 1.3+ FASTQ-like format\n");
 		fprintf(stderr, "         -b        the input read file is in the BAM format\n");
 		fprintf(stderr, "         -0        use single-end reads only (effective with -b)\n");
 		fprintf(stderr, "         -1        use the 1st read in a pair (effective with -b)\n");

bwtaln.h

@@ -87,6 +87,7 @@ typedef struct {
 #define BWA_MODE_BAM_SE     0x40
 #define BWA_MODE_BAM_READ1  0x80
 #define BWA_MODE_BAM_READ2  0x100
+#define BWA_MODE_IL13       0x200
 
 typedef struct {
 	int s_mm, s_gapo, s_gape;

main.c

@@ -3,7 +3,7 @@
 #include "main.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.5.9rc1-9"
+#define PACKAGE_VERSION "0.5.9rc1-r10"
 #endif
 
 static int usage()