X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_sort.c;h=c46bce3b3f4ab2fbc5e5166b4bfaf2ff12b013a9;hb=efc19a36de7236c21b3ae1fe7601e0503bc9c4b7;hp=0ad9cff80ad2a7d6ae9c5c21397622f124c5ed78;hpb=81b4ff832414380351f72ca733ca6a4dfdaed9ff;p=samtools.git

diff --git a/bam_sort.c b/bam_sort.c
index 0ad9cff..c46bce3 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -319,6 +319,40 @@ int bam_merge(int argc, char *argv[])
 
 typedef bam1_t *bam1_p;
 
+static int change_SO(bam_header_t *h, const char *so)
+{
+	char *p, *q, *beg = 0, *end = 0, *newtext;
+	if (h->l_text > 3) {
+		if (strncmp(h->text, "@HD", 3) == 0) {
+			if ((p = strchr(h->text, '\n')) == 0) return -1;
+			*p = '\0';
+			if ((q = strstr(h->text, "\tSO:")) != 0) {
+				*p = '\n'; // change back
+				if (strncmp(q + 4, so, p - q - 4) != 0) {
+					beg = q;
+					for (q += 4; *q != '\n' && *q != '\t'; ++q);
+					end = q;
+				} else return 0; // no need to change
+			} else beg = end = p, *p = '\n';
+		}
+	}
+	if (beg == 0) { // no @HD
+		h->l_text += strlen(so) + 15;
+		newtext = malloc(h->l_text + 1);
+		sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so);
+		strcat(newtext, h->text);
+	} else { // has @HD but different or no SO
+		h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
+		newtext = malloc(h->l_text + 1);
+		strncpy(newtext, h->text, beg - h->text);
+		sprintf(newtext + (beg - h->text), "\tSO:%s", so);
+		strcat(newtext, end);
+	}
+	free(h->text);
+	h->text = newtext;
+	return 0;
+}
+
 static inline int bam1_lt(const bam1_p a, const bam1_p b)
 {
 	if (g_is_by_qname) {
@@ -400,12 +434,13 @@ static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, c
   @param  prefix   prefix of the output and the temporary files; upon
 	                   sucessess, prefix.bam will be written.
   @param  max_mem  approxiate maximum memory (very inaccurate)
+  @param full_path the given output path is the full path and not just the prefix
 
   @discussion It may create multiple temporary subalignment files
   and then merge them by calling bam_merge_core(). This function is
   NOT thread safe.
  */
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path)
 {
 	int ret, i, n_files = 0;
 	size_t mem, max_k, k, max_mem;
@@ -413,6 +448,8 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 	bamFile fp;
 	bam1_t *b, **buf;
 	char *fnout = 0;
+	char const *suffix = ".bam";
+	if (full_path) suffix += 4;
 
 	if (n_threads < 2) n_threads = 1;
 	g_is_by_qname = is_by_qname;
@@ -425,6 +462,8 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 		return;
 	}
 	header = bam_header_read(fp);
+	if (is_by_qname) change_SO(header, "queryname");
+	else change_SO(header, "coordinate");
 	// write sub files
 	for (;;) {
 		if (k == max_k) {
@@ -436,6 +475,11 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 		if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
 		b = buf[k];
 		if ((ret = bam_read1(fp, b)) < 0) break;
+		if (b->data_len < b->m_data>>2) { // shrink
+			b->m_data = b->data_len;
+			kroundup32(b->m_data);
+			b->data = realloc(b->data, b->m_data);
+		}
 		mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
 		++k;
 		if (mem >= max_mem) {
@@ -448,7 +492,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 	// output file name
 	fnout = calloc(strlen(prefix) + 20, 1);
 	if (is_stdout) sprintf(fnout, "-");
-	else sprintf(fnout, "%s.bam", prefix);
+	else sprintf(fnout, "%s%s", prefix, suffix);
 	// write the final output
 	if (n_files == 0) { // a single block
 		char mode[8];
@@ -463,7 +507,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 		fns = (char**)calloc(n_files, sizeof(char*));
 		for (i = 0; i < n_files; ++i) {
 			fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
-			sprintf(fns[i], "%s.%.4d.bam", prefix, i);
+			sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
 		}
 		bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
 		for (i = 0; i < n_files; ++i) {
@@ -486,15 +530,16 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 
 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
 {
-	bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);
+	bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
 }
 
 int bam_sort(int argc, char *argv[])
 {
 	size_t max_mem = 768<<20; // 512MB
-	int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;
-	while ((c = getopt(argc, argv, "nom:@:l:")) >= 0) {
+	int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
+	while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
 		switch (c) {
+		case 'f': full_path = 1; break;
 		case 'o': is_stdout = 1; break;
 		case 'n': is_by_qname = 1; break;
 		case 'm': {
@@ -513,6 +558,7 @@ int bam_sort(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Usage:   samtools sort [options] <in.bam> <out.prefix>\n\n");
 		fprintf(stderr, "Options: -n        sort by read name\n");
+		fprintf(stderr, "         -f        use <out.prefix> as full file name instead of prefix\n");
 		fprintf(stderr, "         -o        final output to stdout\n");
 		fprintf(stderr, "         -l INT    compression level, from 0 to 9 [-1]\n");
 		fprintf(stderr, "         -@ INT    number of sorting and compression threads [1]\n");
@@ -520,6 +566,6 @@ int bam_sort(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		return 1;
 	}
-	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
+	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
 	return 0;
 }