* samtools-0.1.7-17 (r596)

 * also keep the number of coor-less reads in the index file

diff --git a/ChangeLog b/ChangeLog
index 2e6f5354e1856a47094ab14181e6ae103291eb0b..9c6c299f4a1e6cc7bd6ef382b395fd2f50d01668 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,43 @@
+------------------------------------------------------------------------
+r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-16 (r595)
+ * write additional information to bam index
+
+------------------------------------------------------------------------
+r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+fixed a bug for unmapped sequences in indexing
+
+------------------------------------------------------------------------
+r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/samtools.1
+
+rename iterf as iter
+
+------------------------------------------------------------------------
+r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-15 (r592)
+ * fixed a few minor memory leaks in the new pileup code
+ * improved the functionality of mpileup
+
 ------------------------------------------------------------------------
 r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
 Changed paths:

diff --git a/bam_index.c b/bam_index.c
index 074f918752209e90f50b9082f9bb93e5f4a7f2af..3fa950d5235297c36c598258ce20b80183b3f04b 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -65,6 +65,7 @@ KHASH_MAP_INIT_INT(i, bam_binlist_t)
 
 struct __bam_index_t {
        int32_t n;
+       uint64_t n_no_coor; // unmapped reads without coordinate
        khash_t(i) **index;
        bam_lidx_t *index2;
 };
@@ -156,7 +157,7 @@ bam_index_t *bam_index_core(bamFile fp)
        uint32_t last_bin, save_bin;
        int32_t last_coor, last_tid, save_tid;
        bam1_core_t *c;
-       uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end;
+       uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
        idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
        b = (bam1_t*)calloc(1, sizeof(bam1_t));
@@ -171,9 +172,10 @@ bam_index_t *bam_index_core(bamFile fp)
 
        save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
        save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
-    n_mapped = n_unmapped = off_end = 0;
+    n_mapped = n_unmapped = n_no_coor = off_end = 0;
        off_beg = off_end = bam_tell(fp);
        while ((ret = bam_read1(fp, b)) >= 0) {
+               if (c->tid < 0) ++n_no_coor;
                if (last_tid != c->tid) { // change of chromosomes
                        last_tid = c->tid;
                        last_bin = 0xffffffffu;
@@ -208,11 +210,18 @@ bam_index_t *bam_index_core(bamFile fp)
                last_off = bam_tell(fp);
                last_coor = b->core.pos;
        }
-       if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+       if (save_tid >= 0) {
+               insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
+               insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+               insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
+       }
        merge_chunks(idx);
        fill_missing(idx);
+       if (ret >= 0)
+               while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
        if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
        free(b->data); free(b);
+       idx->n_no_coor = n_no_coor;
        return idx;
 }
 
@@ -290,6 +299,11 @@ void bam_index_save(const bam_index_t *idx, FILE *fp)
                                bam_swap_endian_8p(&index2->offset[x]);
                } else fwrite(index2->offset, 8, index2->n, fp);
        }
+       { // write the number of reads coor-less records.
+               uint64_t x = idx->n_no_coor;
+               if (bam_is_be) bam_swap_endian_8p(&x);
+               fwrite(&x, 8, 1, fp);
+       }
        fflush(fp);
 }
 
@@ -351,6 +365,8 @@ static bam_index_t *bam_index_load_core(FILE *fp)
                if (bam_is_be)
                        for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
        }
+       if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0;
+       if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor);
        return idx;
 }
 
@@ -488,7 +504,7 @@ int bam_idxstats(int argc, char *argv[])
        bam_index_t *idx;
        bam_header_t *header;
        bamFile fp;
-       int i;
+       int i, no_stats = 0;
        if (argc < 2) {
                fprintf(stderr, "Usage: samtools idxstats <in.bam>\n");
                return 1;
@@ -506,8 +522,12 @@ int bam_idxstats(int argc, char *argv[])
                k = kh_get(i, h, BAM_MAX_BIN);
                if (k != kh_end(h))
                        printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
+               else no_stats = 1;
                putchar('\n');
        }
+       printf("*\t0");
+       if (!no_stats) printf("\t0\t%llu", (long long)idx->n_no_coor);
+       putchar('\n');
        bam_header_destroy(header);
        bam_index_destroy(idx);
        return 0;

diff --git a/bamtk.c b/bamtk.c
index 2f5970ef1547d1ba1a4fc8a76e1f230aacd7af92..bbeca39b5eea8adc5e8b4a9675df272adb3a9a98 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-16 (r595)"
+#define PACKAGE_VERSION "0.1.7-17 (r596)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);