* samtools-0.1.5-11 (r408)

 * force to overwirte existing MD if it is different from the one calculated
   from fillmd.
 * bgzf.c: improved the compatibility with Windows headers

diff --git a/bam_md.c b/bam_md.c
index 45bb1db7531202caba7a68f5084fd58fa77de710..ead2346e4ec21f75b8ceb88a4b78690d2a3d3b39 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -59,7 +59,7 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
        ksprintf(str, "%d", u);
        if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        else if (nm != old_nm_i) {
-               fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d != %d\n", bam1_qname(b), old_nm_i, nm);
+               fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
                bam_aux_del(b, old_nm);
                bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        }
@@ -72,8 +72,11 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
                                        break;
                        if (i < str->l) is_diff = 1;
                } else is_diff = 1;
-               if (is_diff)
-                       fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' != '%s'\n", bam1_qname(b), old_md+1, str->s);
+               if (is_diff) {
+                       fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
+                       bam_aux_del(b, old_md);
+                       bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+               }
        }
        free(str->s); free(str);
 }

diff --git a/bam_tview.c b/bam_tview.c
index c6a31cd7fc73d20797d3c1d7e1d0fd4545cf8942..441a1b4c9581a628735713cfc1464e87c548ff95 100644 (file)
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -384,8 +384,9 @@ int bam_tview_main(int argc, char *argv[])
        tv_destroy(tv);
        return 0;
 }
-#else // #ifdef NCURSES_VERSION
-#warning "The ncurses library is unavailable; tview is disabled."
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview is disabled."
 int bam_tview_main(int argc, char *argv[])
 {
        fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");

diff --git a/bamtk.c b/bamtk.c
index f162bc3fc82591de805cb3bb1b56f79991f0ea9d..bbdf82c132dd64a82c0ee47353577b84698a5d29 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-10 (r407)"
+#define PACKAGE_VERSION "0.1.5-11 (r408)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -85,7 +85,7 @@ static int usage()
        fprintf(stderr, "         rmdup       remove PCR duplicates\n");
        fprintf(stderr, "         glfview     print GLFv3 file\n");
        fprintf(stderr, "         flagstat    simple stats\n");
-       fprintf(stderr, "         fillmd      fill the MD/NM tag and generate '=' bases\n");
+       fprintf(stderr, "         fillmd      recalculate MD/NM tags and '=' bases\n");
        fprintf(stderr, "\n");
        return 1;
 }

diff --git a/bgzf.c b/bgzf.c
index 364ca64cae7069aa61cb2d5154497575aa1627cd..71d8c81460044cb8b88c655d41ba918874641f61 100644 (file)
--- a/bgzf.c
+++ b/bgzf.c
@@ -39,7 +39,7 @@ extern off_t ftello(FILE *stream);
 extern int fseeko(FILE *stream, off_t offset, int whence);
 #endif
 
-typedef int8_t byte;
+typedef int8_t bgzf_byte_t;
 
 static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
 static const int MAX_BLOCK_SIZE = 64 * 1024;
@@ -86,9 +86,9 @@ packInt32(uint8_t* buffer, uint32_t value)
     buffer[3] = value >> 24;
 }
 
-inline
+static inline
 int
-min(int x, int y)
+bgzf_min(int x, int y)
 {
     return (x < y) ? x : y;
 }
@@ -211,7 +211,7 @@ deflate_block(BGZF* fp, int block_length)
     // Deflate the block in fp->uncompressed_block into fp->compressed_block.
     // Also adds an extra field that stores the compressed block length.
 
-    byte* buffer = fp->compressed_block;
+    bgzf_byte_t* buffer = fp->compressed_block;
     int buffer_size = fp->compressed_block_size;
 
     // Init gzip header
@@ -342,10 +342,10 @@ inflate_block(BGZF* fp, int block_length)
 
 static
 int
-check_header(const byte* header)
+check_header(const bgzf_byte_t* header)
 {
     return (header[0] == GZIP_ID1 &&
-            header[1] == (byte) GZIP_ID2 &&
+            header[1] == (bgzf_byte_t) GZIP_ID2 &&
             header[2] == Z_DEFLATED &&
             (header[3] & FLG_FEXTRA) != 0 &&
             unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
@@ -415,7 +415,7 @@ static
 int
 read_block(BGZF* fp)
 {
-    byte header[BLOCK_HEADER_LENGTH];
+    bgzf_byte_t header[BLOCK_HEADER_LENGTH];
        int size = 0;
 #ifdef _USE_KNETFILE
     int64_t block_address = knet_tell(fp->x.fpr);
@@ -440,7 +440,7 @@ read_block(BGZF* fp)
         return -1;
     }
     int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
-    byte* compressed_block = (byte*) fp->compressed_block;
+    bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
     memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
     int remaining = block_length - BLOCK_HEADER_LENGTH;
 #ifdef _USE_KNETFILE
@@ -479,7 +479,7 @@ bgzf_read(BGZF* fp, void* data, int length)
     }
 
     int bytes_read = 0;
-    byte* output = data;
+    bgzf_byte_t* output = data;
     while (bytes_read < length) {
         int available = fp->block_length - fp->block_offset;
         if (available <= 0) {
@@ -491,8 +491,8 @@ bgzf_read(BGZF* fp, void* data, int length)
                 break;
             }
         }
-        int copy_length = min(length-bytes_read, available);
-        byte* buffer = fp->uncompressed_block;
+        int copy_length = bgzf_min(length-bytes_read, available);
+        bgzf_byte_t* buffer = fp->uncompressed_block;
         memcpy(output, buffer + fp->block_offset, copy_length);
         fp->block_offset += copy_length;
         output += copy_length;
@@ -545,12 +545,12 @@ bgzf_write(BGZF* fp, const void* data, int length)
         fp->uncompressed_block = malloc(fp->uncompressed_block_size);
     }
 
-    const byte* input = data;
+    const bgzf_byte_t* input = data;
     int block_length = fp->uncompressed_block_size;
     int bytes_written = 0;
     while (bytes_written < length) {
-        int copy_length = min(block_length - fp->block_offset, length - bytes_written);
-        byte* buffer = fp->uncompressed_block;
+        int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
+        bgzf_byte_t* buffer = fp->uncompressed_block;
         memcpy(buffer + fp->block_offset, input, copy_length);
         fp->block_offset += copy_length;
         input += copy_length;