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root/gclib/tophat_cpp/bam2fastx.cpp

#	Line 10 | Line 10
10		bool sam_input=false; //default is BAM
11		bool all_reads=false;
12		bool mapped_only=false;
13	+	char outfname[1024];
14
15		#define USAGE "Usage: bam2fastx [--fasta|-a|--fastq|-q] [--sam|-s|-t] \n\
16	<	[-M|--mapped-only|-A|--all] <in.bam>|<in.sam> \n"
16	>	[-M|--mapped-only|-A|--all] [-o <outfile>] <in.bam>|<in.sam> \n"
17
18
19
20		char qseq[2048];
21
22	<	const char *short_options = "aqstMU";
22	>	const char *short_options = "o:aqstMUA";
23
24		enum {
25		OPT_FASTA = 127,
#	Line 67 | Line 68
68		case OPT_ALL:
69		all_reads = true;
70		break;
71	+	case 'o':
72	+	strcpy(outfname, optarg);
73	+	break;
74		default:
75		return 1;
76		}
#	Line 80 | Line 84
84
85		#define bam_unmapped(b) (((b)->core.flag & BAM_FUNMAP) != 0)
86
87	<	void showfastq(const bam1_t *b, samfile_t* fp) {
87	>	void showfastq(const bam1_t *b, samfile_t* fp, FILE* fout) {
88		char *name  = bam1_qname(b);
89		char *qual  = (char*)bam1_qual(b);
90		char *s    = (char*)bam1_seq(b);
#	Line 95 | Line 99
99		}
100		qseq[i] = 0;
101
102	<	printf("@%s\n%s\n",name, qseq);
102	>	fprintf(fout, "@%s\n%s\n",name, qseq);
103		for(i=0;i<(b->core.l_qseq);i++) {
104		qseq[i]=qual[i]+33;
105		}
106		qseq[i]=0;
107	<	printf("+\n%s\n",qseq);
107	>	fprintf(fout, "+\n%s\n",qseq);
108		}
109
110	<	void showfasta(const bam1_t *b, samfile_t* fp) {
110	>	void showfasta(const bam1_t *b, samfile_t* fp, FILE* fout) {
111		char *name  = bam1_qname(b);
112		char *s    = (char*)bam1_seq(b);
113		int i;
#	Line 112 | Line 116
116		qseq[i] = bam_nt16_rev_table[v];
117		}
118		qseq[i] = 0;
119	<	printf(">%s\n%s\n",name, qseq);
119	>	fprintf(fout, ">%s\n%s\n",name, qseq);
120		}
121
122
#	Line 120 | Line 124
124		int main(int argc, char *argv[])
125		{
126		samfile_t *fp;
127	+	outfname[0]=0;
128		char* fname=NULL;
129
130		if (parse_options(argc, argv) || optind>=argc) {
#	Line 140 | Line 145
145		fprintf(stderr, "Error: bam2fastx failed to open BAM file %s\n", fname);
146		return 1;
147		}
148	<
148	>	FILE* fout=stdout;
149	>	if (outfname[0]) {
150	>	fout=fopen(outfname, "w");
151	>	if (fout==NULL) {
152	>	fprintf(stderr, "Error creating output file %s\n", outfname);
153	>	return 2;
154	>	}
155	>	}
156		bam1_t *b = bam_init1();
157		if (is_fastq) {
158	<	while (samread(fp, b) >= 0) showfastq(b, fp);
158	>	while (samread(fp, b) >= 0) showfastq(b, fp, fout);
159		}
160		else {
161	<	while (samread(fp, b) >= 0) showfasta(b, fp);
161	>	while (samread(fp, b) >= 0) showfasta(b, fp, fout);
162		}
163
164		bam_destroy1(b);

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