X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_sort.c;h=7d00cd1a83321729c1384cf56f066d2c83f65548;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=6c3f52d17ce4dc0dfd8c9d1277cf8050c7e267ca;hpb=d07731e7c769ac5f2709ac60eb60ddd3fa0120fd;p=samtools.git

diff --git a/bam_sort.c b/bam_sort.c
index 6c3f52d..7d00cd1 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -288,6 +288,7 @@ int bam_merge(int argc, char *argv[])
 		fprintf(stderr, "         -u       uncompressed BAM output\n");
 		fprintf(stderr, "         -f       overwrite the output BAM if exist\n");
 		fprintf(stderr, "         -1       compress level 1\n");
+		fprintf(stderr, "         -l INT   compression level, from 0 to 9 [-1]\n");
 		fprintf(stderr, "         -@ INT   number of BAM compression threads [0]\n");
 		fprintf(stderr, "         -R STR   merge file in the specified region STR [all]\n");
 		fprintf(stderr, "         -h FILE  copy the header in FILE to <out.bam> [in1.bam]\n\n");
@@ -318,6 +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) {
@@ -406,7 +441,7 @@ static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, c
  */
 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 ret, i, extra_mem, n_files = 0;
+	int ret, i, n_files = 0;
 	size_t mem, max_k, k, max_mem;
 	bam_header_t *header;
 	bamFile fp;
@@ -414,7 +449,6 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 	char *fnout = 0;
 
 	if (n_threads < 2) n_threads = 1;
-	extra_mem = sizeof(void*) + sizeof(void*) + (sizeof(bam1_t) - sizeof(bam1_core_t));
 	g_is_by_qname = is_by_qname;
 	max_k = k = 0; mem = 0;
 	max_mem = _max_mem * n_threads;
@@ -425,6 +459,8 @@ 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) {
@@ -436,7 +472,12 @@ 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;
-		mem += ret + extra_mem;
+		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) {
 			n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
@@ -510,7 +551,14 @@ int bam_sort(int argc, char *argv[])
 		}
 	}
 	if (optind + 2 > argc) {
-		fprintf(stderr, "Usage: samtools sort [-on] [-m maxMem=1G] <in.bam> <out.prefix>\n");
+		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, "         -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");
+		fprintf(stderr, "         -m INT    max memory per thread; suffix K/M/G recognized [768M]\n");
+		fprintf(stderr, "\n");
 		return 1;
 	}
 	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);