Unsuccessful attempt to get correct lengths

pysam-developers · Nov 11, 2018 · fea8c81 · fea8c81
1 parent e4b34cd
commit fea8c81
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Showing 7 changed files with 12 additions and 12 deletions.
diff --git a/htslib/cram/cram_samtools.c b/htslib/cram/cram_samtools.c
@@ -139,7 +139,7 @@ bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
     header->n_targets = h->nref;
     header->target_name = (char **)calloc(header->n_targets,
                                           sizeof(char *));
-    header->target_len = (uint32_t *)calloc(header->n_targets, 4);
+    header->target_len = (uint64_t *)calloc(header->n_targets, 4);
 
     for (i = 0; i < h->nref; i++) {
         header->target_name[i] = strdup(h->ref[i].name);

diff --git a/htslib/htslib/sam.h b/htslib/htslib/sam.h
@@ -54,7 +54,7 @@ extern "C" {
 typedef struct {
     int32_t n_targets, ignore_sam_err;
     uint32_t l_text;
-    uint32_t *target_len;
+    uint64_t *target_len;
     int8_t *cigar_tab;
     char **target_name;
     char *text;

diff --git a/htslib/sam.c b/htslib/sam.c
@@ -87,7 +87,7 @@ bam_hdr_t *bam_hdr_dup(const bam_hdr_t *h0)
     // TODO Check for memory allocation failures
     h->text = (char*)calloc(h->l_text + 1, 1);
     memcpy(h->text, h0->text, h->l_text);
-    h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
+    h->target_len = (uint64_t*)calloc(h->n_targets, sizeof(uint64_t));
     h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
     int i;
     for (i = 0; i < h->n_targets; ++i) {
@@ -106,12 +106,12 @@ static bam_hdr_t *hdr_from_dict(sdict_t *d)
     h->sdict = d;
     h->n_targets = kh_size(d);
     // TODO Check for memory allocation failures
-    h->target_len = (uint32_t*)malloc(sizeof(uint32_t) * h->n_targets);
+    h->target_len = (uint64_t*)malloc(sizeof(uint64_t) * h->n_targets);
     h->target_name = (char**)malloc(sizeof(char*) * h->n_targets);
     for (k = kh_begin(d); k != kh_end(d); ++k) {
         if (!kh_exist(d, k)) continue;
         h->target_name[kh_val(d, k)>>32] = (char*)kh_key(d, k);
-        h->target_len[kh_val(d, k)>>32]  = kh_val(d, k) & 0xffffffffUL;
+        h->target_len[kh_val(d, k)>>64]  = kh_val(d, k) & 0xffffffffffffffffUL;
         kh_val(d, k) >>= 32;
     }
     return h;
@@ -164,7 +164,7 @@ bam_hdr_t *bam_hdr_read(BGZF *fp)
     if (h->n_targets > 0) {
         h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
         if (!h->target_name) goto nomem;
-        h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
+        h->target_len = (uint64_t*)calloc(h->n_targets, sizeof(uint64_t));
         if (!h->target_len) goto nomem;
     }
     else {

diff --git a/pysam/libcalignmentfile.pyx b/pysam/libcalignmentfile.pyx
@@ -248,7 +248,7 @@ cdef class AlignmentHeader(object):
             if self.ptr.target_name == NULL:
                 raise MemoryError("could not allocate {} bytes".format(n, sizeof(char *)))
 
-            self.ptr.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
+            self.ptr.target_len = <uint64_t*>calloc(n, sizeof(uint64_t))
             if self.ptr.target_len == NULL:
                 raise MemoryError("could not allocate {} bytes".format(n, sizeof(uint32_t)))
 

diff --git a/pysam/libchtslib.pxd b/pysam/libchtslib.pxd
@@ -857,7 +857,7 @@ cdef extern from "htslib/sam.h" nogil:
     ctypedef struct bam_hdr_t:
          int32_t n_targets, ignore_sam_err
          uint32_t l_text
-         uint32_t *target_len
+         uint64_t *target_len
          uint8_t *cigar_tab
          char **target_name
          char *text

diff --git a/samtools/test/merge/test_trans_tbl_init.c b/samtools/test/merge/test_trans_tbl_init.c
@@ -76,7 +76,7 @@ bam_hdr_t * setup_test(const char *bam0_header_text,
     bam0->l_text = strlen(bam0_header_text);
     bam0->n_targets = 1;
     bam0->target_name = (char**)calloc(bam0_n_refseqs, sizeof(char*));
-    bam0->target_len = (uint32_t*)calloc(bam0_n_refseqs, sizeof(uint32_t));
+    bam0->target_len = (uint64_t*)calloc(bam0_n_refseqs, sizeof(uint64_t));
     for (i = 0; i < bam0_n_refseqs; i++) {
         bam0->target_name[i] = strdup(bam0_refseqs[i].name);
         if (!bam0->target_name[i]) goto fail;
@@ -92,7 +92,7 @@ bam_hdr_t * setup_test(const char *bam0_header_text,
     bam1->l_text = strlen(bam1_header_text);
     bam1->n_targets = bam1_n_refseqs;
     bam1->target_name = (char**)calloc(bam1_n_refseqs, sizeof(char*));
-    bam1->target_len = (uint32_t*)calloc(bam1_n_refseqs, sizeof(uint32_t));
+    bam1->target_len = (uint64_t*)calloc(bam1_n_refseqs, sizeof(uint64_t));
     for (i = 0; i < bam1_n_refseqs; i++) {
         bam1->target_name[i] = strdup(bam1_refseqs[i].name);
         if (!bam1->target_name[i]) goto fail;

diff --git a/samtools/test/merge/test_trans_tbl_init.c.pysam.c b/samtools/test/merge/test_trans_tbl_init.c.pysam.c
@@ -78,7 +78,7 @@ bam_hdr_t * setup_test(const char *bam0_header_text,
     bam0->l_text = strlen(bam0_header_text);
     bam0->n_targets = 1;
     bam0->target_name = (char**)calloc(bam0_n_refseqs, sizeof(char*));
-    bam0->target_len = (uint32_t*)calloc(bam0_n_refseqs, sizeof(uint32_t));
+    bam0->target_len = (uint64_t*)calloc(bam0_n_refseqs, sizeof(uint64_t));
     for (i = 0; i < bam0_n_refseqs; i++) {
         bam0->target_name[i] = strdup(bam0_refseqs[i].name);
         if (!bam0->target_name[i]) goto fail;
@@ -94,7 +94,7 @@ bam_hdr_t * setup_test(const char *bam0_header_text,
     bam1->l_text = strlen(bam1_header_text);
     bam1->n_targets = bam1_n_refseqs;
     bam1->target_name = (char**)calloc(bam1_n_refseqs, sizeof(char*));
-    bam1->target_len = (uint32_t*)calloc(bam1_n_refseqs, sizeof(uint32_t));
+    bam1->target_len = (uint64_t*)calloc(bam1_n_refseqs, sizeof(uint64_t));
     for (i = 0; i < bam1_n_refseqs; i++) {
         bam1->target_name[i] = strdup(bam1_refseqs[i].name);
         if (!bam1->target_name[i]) goto fail;