X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fsam_view.c.pysam.c;h=2c4736336ee2e27150ce47d15d661e190c580888;hp=05da8e3e5a51dd157b2ffcdb250e4b045f0a7e8c;hb=e1756c41e7a1d7cc01fb95e42df9dd04da2d2991;hpb=ca46ef4ba4a883c57cea62d5bf1bc021f1185109

diff --git a/samtools/sam_view.c.pysam.c b/samtools/sam_view.c.pysam.c
index 05da8e3..2c47363 100644
--- a/samtools/sam_view.c.pysam.c
+++ b/samtools/sam_view.c.pysam.c
@@ -21,28 +21,39 @@ typedef struct {
 
 typedef khash_t(rg) *rghash_t;
 
-// FIXME: we'd better use no global variables...
 static rghash_t g_rghash = 0;
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
-static float g_subsam = -1;
 static char *g_library, *g_rg;
+static int g_sol2sanger_tbl[128];
 static void *g_bed;
 
 void *bed_read(const char *fn);
 void bed_destroy(void *_h);
 int bed_overlap(const void *_h, const char *chr, int beg, int end);
 
+static void sol2sanger(bam1_t *b)
+{
+	int l;
+	uint8_t *qual = bam1_qual(b);
+	if (g_sol2sanger_tbl[30] == 0) {
+		for (l = 0; l != 128; ++l) {
+			g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
+			if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
+		}
+	}
+	for (l = 0; l < b->core.l_qseq; ++l) {
+		int q = qual[l];
+		if (q > 127) q = 127;
+		qual[l] = g_sol2sanger_tbl[q];
+	}
+}
+
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
 	if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
 		return 1;
 	if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
 		return 1;
-	if (g_subsam > 0.) {
-		int x = (int)(g_subsam + .499);
-		uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
-		if (k%1024 / 1024.0 >= g_subsam - x) return 1;
-	}
 	if (g_rg || g_rghash) {
 		uint8_t *s = bam_aux_get(b, "RG");
 		if (s) {
@@ -112,7 +123,7 @@ static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {
-	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
+	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
 	int of_type = BAM_OFDEC, is_long_help = 0;
 	int count = 0;
 	samfile_t *in = 0, *out = 0;
@@ -120,10 +131,10 @@ int main_samview(int argc, char *argv[])
 
 	/* parse command-line options */
 	strcpy(in_mode, "r"); strcpy(out_mode, "w");
-	while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {
+	while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
 		switch (c) {
-		case 's': g_subsam = atof(optarg); break;
 		case 'c': is_count = 1; break;
+		case 'C': slx2sngr = 1; break;
 		case 'S': is_bamin = 0; break;
 		case 'b': is_bamout = 1; break;
 		case 't': fn_list = strdup(optarg); is_bamin = 0; break;
@@ -207,6 +218,7 @@ int main_samview(int argc, char *argv[])
 		int r;
 		while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
 			if (!__g_skip_aln(in->header, b)) {
+				if (slx2sngr) sol2sanger(b);
 				if (!is_count) samwrite(out, b); // write the alignment to `out'
 				count++;
 			}
@@ -289,7 +301,6 @@ static int usage(int is_long_help)
 	fprintf(pysamerr, "         -q INT   minimum mapping quality [0]\n");
 	fprintf(pysamerr, "         -l STR   only output reads in library STR [null]\n");
 	fprintf(pysamerr, "         -r STR   only output reads in read group STR [null]\n");
-	fprintf(pysamerr, "         -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
 	fprintf(pysamerr, "         -?       longer help\n");
 	fprintf(pysamerr, "\n");
 	if (is_long_help)
@@ -340,69 +351,3 @@ int main_import(int argc, char *argv[])
 	free(argv2);
 	return ret;
 }
-
-int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
-
-int main_bam2fq(int argc, char *argv[])
-{
-	bamFile fp;
-	bam_header_t *h;
-	bam1_t *b;
-	int8_t *buf;
-	int max_buf;
-	if (argc == 1) {
-		fprintf(pysamerr, "Usage: samtools bam2fq <in.bam>\n");
-		return 1;
-	}
-	fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
-	if (fp == 0) return 1;
-	h = bam_header_read(fp);
-	b = bam_init1();
-	buf = 0;
-	max_buf = 0;
-	while (bam_read1(fp, b) >= 0) {
-		int i, qlen = b->core.l_qseq;
-		uint8_t *seq;
-		putchar('@'); fputs(bam1_qname(b), stdout);
-		if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
-		else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
-		else putchar('\n');
-		if (max_buf < qlen + 1) {
-			max_buf = qlen + 1;
-			kroundup32(max_buf);
-			buf = realloc(buf, max_buf);
-		}
-		buf[qlen] = 0;
-		seq = bam1_seq(b);
-		for (i = 0; i < qlen; ++i)
-			buf[i] = bam1_seqi(seq, i);
-		if (b->core.flag & 16) { // reverse complement
-			for (i = 0; i < qlen>>1; ++i) {
-				int8_t t = seq_comp_table[buf[qlen - 1 - i]];
-				buf[qlen - 1 - i] = seq_comp_table[buf[i]];
-				buf[i] = t;
-			}
-			if (qlen&1) buf[i] = seq_comp_table[buf[i]];
-		}
-		for (i = 0; i < qlen; ++i)
-			buf[i] = bam_nt16_rev_table[buf[i]];
-		puts((char*)buf);
-		puts("+");
-		seq = bam1_qual(b);
-		for (i = 0; i < qlen; ++i)
-			buf[i] = 33 + seq[i];
-		if (b->core.flag & 16) { // reverse
-			for (i = 0; i < qlen>>1; ++i) {
-				int8_t t = buf[qlen - 1 - i];
-				buf[qlen - 1 - i] = buf[i];
-				buf[i] = t;
-			}
-		}
-		puts((char*)buf);
-	}
-	free(buf);
-	bam_destroy1(b);
-	bam_header_destroy(h);
-	bam_close(fp);
-	return 0;
-}