From 925ddfb6973c77f51940c077bf7f20b663d9bb5f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 11 Dec 2014 10:38:36 -0500
Subject: [PATCH] r1025: accept file with -H; allow to replace @SQ

---
 bwa.c     | 14 +++++++++++---
 fastmap.c | 18 ++++++++++++++++--
 main.c    |  2 +-
 3 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/bwa.c b/bwa.c
index 2411b4a..6739edd 100644
--- a/bwa.c
+++ b/bwa.c
@@ -369,10 +369,18 @@ int bwa_idx2mem(bwaidx_t *idx)
 
 void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
 {
-	int i;
+	int i, n_SQ = 0;
+	const char *p = hdr_line;
 	extern char *bwa_pg;
-	for (i = 0; i < bns->n_seqs; ++i)
-		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+	while ((p = strstr(p, "@SQ\t")) != 0) {
+		if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
+		p += 4;
+	}
+	if (n_SQ == 0) {
+		for (i = 0; i < bns->n_seqs; ++i)
+			err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+	} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
+		fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
 	if (hdr_line) err_printf("%s\n", hdr_line);
 	if (bwa_pg) err_printf("%s\n", bwa_pg);
 }
diff --git a/fastmap.c b/fastmap.c
index 537fff7..79ebd39 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -192,7 +192,21 @@ int main_mem(int argc, char *argv[])
 		} else if (c == 'R') {
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
 		} else if (c == 'H') {
-			hdr_line = bwa_insert_header(optarg, hdr_line);
+			if (optarg[0] != '@') {
+				FILE *fp;
+				if ((fp = fopen(optarg, "r")) != 0) {
+					char *buf;
+					buf = calloc(1, 0x10000);
+					while (fgets(buf, 0xffff, fp)) {
+						i = strlen(buf);
+						assert(buf[i-1] == '\n'); // a long line
+						buf[i-1] = 0;
+						hdr_line = bwa_insert_header(buf, hdr_line);
+					}
+					free(buf);
+					fclose(fp);
+				}
+			} else hdr_line = bwa_insert_header(optarg, hdr_line);
 		} else if (c == 'I') { // specify the insert size distribution
 			aux.pes0 = pes;
 			pes[1].failed = 0;
@@ -253,7 +267,7 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "\nInput/output options:\n\n");
 		fprintf(stderr, "       -p            smart pairing (ignoring in2.fq)\n");
 		fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
-		fprintf(stderr, "       -H STR        insert an arbitrary header line [null]\n");
+		fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
 		fprintf(stderr, "       -j            ignore ALT contigs\n");
 		fprintf(stderr, "\n");
 		fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
diff --git a/main.c b/main.c
index 8216811..2a0118c 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.10-r1017-dirty"
+#define PACKAGE_VERSION "0.7.10-r1025-dirty"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);