print msg to stderr; output more in fastmap

bwt_gen.c

@@ -1486,8 +1486,8 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
 		BWTIncConstruct(bwtInc, textToLoad);
 		processedTextLength += textToLoad;
 		if (bwtInc->numberOfIterationDone % 10 == 0) {
-			printf("[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n",
-				   (long)bwtInc->numberOfIterationDone, (long)processedTextLength);
+			fprintf(stderr, "[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n",
+					(long)bwtInc->numberOfIterationDone, (long)processedTextLength);
 		}
 	}
 	return bwtInc;

fastmap.c

@@ -1,6 +1,8 @@
 #include <zlib.h>
-#include <unistd.h>
 #include <stdio.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include "bntseq.h"
 #include "bwt.h"
 #include "kvec.h"
 #include "kseq.h"
@@ -10,28 +12,37 @@ extern unsigned char nst_nt4_table[256];
 
 int main_fastmap(int argc, char *argv[])
 {
-	int c, i;
+	int c, i, min_iwidth = 3, min_len = 17;
 	kseq_t *seq;
+	bwtint_t k;
 	gzFile fp;
 	bwt_t *bwt;
+	bntseq_t *bns;
 	bwtintv_v a[3], mem, *tvec[3];
-	while ((c = getopt(argc, argv, "")) >= 0) {
+
+	while ((c = getopt(argc, argv, "w:l:")) >= 0) {
 		switch (c) {
+			case 'w': min_iwidth = atoi(optarg); break;
+			case 'l': min_len = atoi(optarg); break;
 		}
 	}
 	if (optind + 1 >= argc) {
 		fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n");
 		return 1;
 	}
+
 	fp = gzopen(argv[optind + 1], "r");
 	seq = kseq_init(fp);
-	{ // load the BWT
+	{ // load the packed sequences, BWT and SA
 		char *tmp = calloc(strlen(argv[optind]) + 5, 1);
 		strcat(strcpy(tmp, argv[optind]), ".bwt");
 		bwt = bwt_restore_bwt(tmp);
+		strcat(strcpy(tmp, argv[optind]), ".sa");
+		bwt_restore_sa(tmp, bwt);
 		free(tmp);
+		bns = bns_restore(argv[optind]);
 	}
-	for (i = 0; i < 3; ++i) {
+	for (i = 0; i < 3; ++i) { // initiate the temporary array
 		kv_init(a[i]);
 		tvec[i] = &a[i];
 	}
@@ -40,15 +51,27 @@ int main_fastmap(int argc, char *argv[])
 		for (i = 0; i < seq->seq.l; ++i)
 			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
 		bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
-		printf(">%s\t%ld\n", seq->name.s, mem.n);
+		printf(">%s\t%ld\n", seq->name.s, seq->seq.l);
 		for (i = 0; i < mem.n; ++i) {
 			bwtintv_t *p = &mem.a[i];
-			printf("%d\t%d\t%ld\n", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
+			if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
+			printf("%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
+			if (p->x[2] <= min_iwidth) {
+				for (k = 0; k < p->x[2]; ++k) {
+					int is_rev;
+					int64_t pos;
+					pos = bns_depos(bns, bwt_sa(bwt, p->x[0] + k), &is_rev);
+					printf("\t%c%ld", is_rev?'-':'+', (long)pos);
+				}
+			}
+			putchar('\n');
 		}
 		puts("//");
 	}
+
 	free(mem.a);
 	for (i = 0; i < 3; ++i) free(a[i].a);
+	bns_destroy(bns);
 	bwt_destroy(bwt);
 	kseq_destroy(seq);
 	gzclose(fp);