X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fbamcheck.c;h=efccf9a112703f7801e5e523598f06ea447f28f7;hb=b224b0da969d8997e573cc0005dc815b704c0398;hp=76a9f6ee04a8247ebbfd93b35a2e1b0c3e1ca8eb;hpb=0ab78ddb98818366103c11330526b8a2ea33a757;p=samtools.git

diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index 76a9f6e..efccf9a 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -12,10 +12,9 @@
             considered, even small overlap is good enough to include the read in the stats.
 */
 
-#define BAMCHECK_VERSION "2012-03-29"
+#define BAMCHECK_VERSION "2012-04-04"
 
 #define _ISOC99_SOURCE
-#define _GNU_SOURCE
 #include <stdio.h>
 #include <stdlib.h>
 #include <stdarg.h>
@@ -282,8 +281,9 @@ void count_indels(stats_t *stats,bam1_t *bam_line)
 
         if ( cig==1 )
         {
-            int idx = is_fwd ? icycle : read_len-icycle-1;
-            if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases);
+            int idx = is_fwd ? icycle : read_len-icycle;
+            if ( idx<0 ) error("FIXME: read_len=%d vs icycle=%d\n", read_len,icycle);
+            if ( idx >= stats->nbases || idx<0 ) error("FIXME: %d vs %d\n", idx,stats->nbases);
             stats->ins_cycles[idx]++;
             icycle += ncig;
             if ( ncig<=stats->nindels )
@@ -292,7 +292,8 @@ void count_indels(stats_t *stats,bam1_t *bam_line)
         }
         if ( cig==2 )
         {
-            int idx = is_fwd ? icycle : read_len-icycle-1;
+            int idx = is_fwd ? icycle-1 : read_len-icycle-1;
+            if ( idx<0 ) continue;  // discard meaningless deletions
             if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases);
             stats->del_cycles[idx]++;
             if ( ncig<=stats->nindels )
@@ -515,15 +516,15 @@ void realloc_buffers(stats_t *stats, int seq_len)
         error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
     memset(stats->deletions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
 
-    stats->ins_cycles = realloc(stats->ins_cycles, n*sizeof(uint64_t));
+    stats->ins_cycles = realloc(stats->ins_cycles, (n+1)*sizeof(uint64_t));
     if ( !stats->ins_cycles )
-        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
-    memset(stats->ins_cycles + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->ins_cycles + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
 
-    stats->del_cycles = realloc(stats->del_cycles, n*sizeof(uint64_t));
+    stats->del_cycles = realloc(stats->del_cycles, (n+1)*sizeof(uint64_t));
     if ( !stats->del_cycles )
-        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
-    memset(stats->del_cycles + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+        error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+    memset(stats->del_cycles + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
 
     stats->nbases = n;
 
@@ -932,7 +933,7 @@ void output_stats(stats_t *stats)
     }
 
     printf("# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions, number of deletions\n");
-    for (ilen=0; ilen<stats->nbases; ilen++)
+    for (ilen=0; ilen<=stats->nbases; ilen++)
     {
         if ( stats->ins_cycles[ilen]>0 || stats->del_cycles[ilen]>0 )
             printf("IC\t%d\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles[ilen], (long)stats->del_cycles[ilen]);
@@ -982,6 +983,40 @@ void output_stats(stats_t *stats)
 
 void bam_init_header_hash(bam_header_t *header);
 
+size_t mygetline(char **line, size_t *n, FILE *fp)
+{
+    if (line == NULL || n == NULL || fp == NULL)
+    {
+        errno = EINVAL;
+        return -1;
+    }
+    if (*n==0 || !*line)
+    {
+        *line = NULL;
+        *n = 0;
+    }
+
+    size_t nread=0;
+    int c;
+    while ((c=getc(fp))!= EOF && c!='\n')
+    {
+        if ( ++nread>=*n )
+        {
+            *n += 255;
+            *line = realloc(*line, sizeof(char)*(*n));
+        }
+        (*line)[nread-1] = c;
+    }
+    if ( nread>=*n )
+    {
+        *n += 255;
+        *line = realloc(*line, sizeof(char)*(*n));
+    }
+    (*line)[nread] = 0;
+    return nread>0 ? nread : -1;
+
+}
+
 void init_regions(stats_t *stats, char *file)
 {
     khiter_t iter;
@@ -998,13 +1033,13 @@ void init_regions(stats_t *stats, char *file)
     ssize_t nread;
     int warned = 0;
     int prev_tid=-1, prev_pos=-1;
-    while ((nread = getline(&line, &len, fp)) != -1) 
+    while ((nread = mygetline(&line, &len, fp)) != -1) 
     {
         if ( line[0] == '#' ) continue;
 
         int i = 0;
         while ( i<nread && !isspace(line[i]) ) i++;
-        if ( i>=nread ) error("Could not parse the file: %s\n", file);
+        if ( i>=nread ) error("Could not parse the file: %s [%s]\n", file,line);
         line[i] = 0;
 
         iter = kh_get(str, header_hash, line);
@@ -1210,8 +1245,8 @@ int main(int argc, char *argv[])
     stats->read_lengths  = calloc(stats->nbases,sizeof(uint64_t));
     stats->insertions    = calloc(stats->nbases,sizeof(uint64_t));
     stats->deletions     = calloc(stats->nbases,sizeof(uint64_t));
-    stats->ins_cycles    = calloc(stats->nbases,sizeof(uint64_t));
-    stats->del_cycles    = calloc(stats->nbases,sizeof(uint64_t));
+    stats->ins_cycles    = calloc(stats->nbases+1,sizeof(uint64_t));
+    stats->del_cycles    = calloc(stats->nbases+1,sizeof(uint64_t));
     if ( targets )
         init_regions(stats, targets);