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>
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 )
}
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 )
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;
printf(" %s",stats->argv[i]);
printf("\n");
printf("# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
- printf("SN\tsequences:\t%ld\n", stats->nreads_1st+stats->nreads_2nd);
+ printf("SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd));
printf("SN\tis paired:\t%d\n", stats->nreads_1st&&stats->nreads_2nd ? 1 : 0);
printf("SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
- printf("SN\t1st fragments:\t%ld\n", stats->nreads_1st);
- printf("SN\tlast fragments:\t%ld\n", stats->nreads_2nd);
- printf("SN\treads mapped:\t%ld\n", stats->nreads_paired+stats->nreads_unpaired);
- printf("SN\treads unmapped:\t%ld\n", stats->nreads_unmapped);
- printf("SN\treads unpaired:\t%ld\n", stats->nreads_unpaired);
- printf("SN\treads paired:\t%ld\n", stats->nreads_paired);
- printf("SN\treads duplicated:\t%ld\n", stats->nreads_dup);
- printf("SN\treads MQ0:\t%ld\n", stats->nreads_mq0);
- printf("SN\ttotal length:\t%ld\n", stats->total_len);
- printf("SN\tbases mapped:\t%ld\n", stats->nbases_mapped);
- printf("SN\tbases mapped (cigar):\t%ld\n", stats->nbases_mapped_cigar);
- printf("SN\tbases trimmed:\t%ld\n", stats->nbases_trimmed);
- printf("SN\tbases duplicated:\t%ld\n", stats->total_len_dup);
- printf("SN\tmismatches:\t%ld\n", stats->nmismatches);
+ printf("SN\t1st fragments:\t%ld\n", (long)stats->nreads_1st);
+ printf("SN\tlast fragments:\t%ld\n", (long)stats->nreads_2nd);
+ printf("SN\treads mapped:\t%ld\n", (long)(stats->nreads_paired+stats->nreads_unpaired));
+ printf("SN\treads unmapped:\t%ld\n", (long)stats->nreads_unmapped);
+ printf("SN\treads unpaired:\t%ld\n", (long)stats->nreads_unpaired);
+ printf("SN\treads paired:\t%ld\n", (long)stats->nreads_paired);
+ printf("SN\treads duplicated:\t%ld\n", (long)stats->nreads_dup);
+ printf("SN\treads MQ0:\t%ld\n", (long)stats->nreads_mq0);
+ printf("SN\ttotal length:\t%ld\n", (long)stats->total_len);
+ printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped);
+ printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar);
+ printf("SN\tbases trimmed:\t%ld\n", (long)stats->nbases_trimmed);
+ printf("SN\tbases duplicated:\t%ld\n", (long)stats->total_len_dup);
+ printf("SN\tmismatches:\t%ld\n", (long)stats->nmismatches);
printf("SN\terror rate:\t%e\n", (float)stats->nmismatches/stats->nbases_mapped_cigar);
float avg_read_length = (stats->nreads_1st+stats->nreads_2nd)?stats->total_len/(stats->nreads_1st+stats->nreads_2nd):0;
printf("SN\taverage length:\t%.0f\n", avg_read_length);
printf("SN\taverage quality:\t%.1f\n", stats->total_len?stats->sum_qual/stats->total_len:0);
printf("SN\tinsert size average:\t%.1f\n", avg_isize);
printf("SN\tinsert size standard deviation:\t%.1f\n", sd_isize);
- printf("SN\tinward oriented pairs:\t%ld\n", nisize_inward);
- printf("SN\toutward oriented pairs:\t%ld\n", nisize_outward);
- printf("SN\tpairs with other orientation:\t%ld\n", nisize_other);
+ printf("SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
+ printf("SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
+ printf("SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
int ibase,iqual;
if ( stats->max_len<stats->nbases ) stats->max_len++;
printf("FFQ\t%d",ibase+1);
for (iqual=0; iqual<=stats->max_qual; iqual++)
{
- printf("\t%ld", stats->quals_1st[ibase*stats->nquals+iqual]);
+ printf("\t%ld", (long)stats->quals_1st[ibase*stats->nquals+iqual]);
}
printf("\n");
}
printf("LFQ\t%d",ibase+1);
for (iqual=0; iqual<=stats->max_qual; iqual++)
{
- printf("\t%ld", stats->quals_2nd[ibase*stats->nquals+iqual]);
+ printf("\t%ld", (long)stats->quals_2nd[ibase*stats->nquals+iqual]);
}
printf("\n");
}
printf("MPC\t%d",ibase+1);
for (iqual=0; iqual<=stats->max_qual; iqual++)
{
- printf("\t%ld", stats->mpc_buf[ibase*stats->nquals+iqual]);
+ printf("\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]);
}
printf("\n");
}
for (ibase=0; ibase<stats->ngc; ibase++)
{
if ( stats->gc_1st[ibase]==stats->gc_1st[ibase_prev] ) continue;
- printf("GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1),stats->gc_1st[ibase_prev]);
+ printf("GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_1st[ibase_prev]);
ibase_prev = ibase;
}
printf("# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.\n");
for (ibase=0; ibase<stats->ngc; ibase++)
{
if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue;
- printf("GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1),stats->gc_2nd[ibase_prev]);
+ printf("GCL\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1), (long)stats->gc_2nd[ibase_prev]);
ibase_prev = ibase;
}
printf("# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%%]\n");
}
printf("# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
for (isize=1; isize<ibulk; isize++)
- printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize,(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
- stats->isize_inward[isize],stats->isize_outward[isize],stats->isize_other[isize]);
+ printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, (long)(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
+ (long)stats->isize_inward[isize], (long)stats->isize_outward[isize], (long)stats->isize_other[isize]);
printf("# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count\n");
int ilen;
for (ilen=0; ilen<stats->max_len; ilen++)
{
if ( stats->read_lengths[ilen]>0 )
- printf("RL\t%d\t%ld\n", ilen,stats->read_lengths[ilen]);
+ printf("RL\t%d\t%ld\n", ilen, (long)stats->read_lengths[ilen]);
}
printf("# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions\n");
for (ilen=0; ilen<stats->nindels; ilen++)
{
if ( stats->insertions[ilen]>0 || stats->deletions[ilen]>0 )
- printf("ID\t%d\t%ld\t%ld\n", ilen+1,stats->insertions[ilen],stats->deletions[ilen]);
+ printf("ID\t%d\t%ld\t%ld\n", ilen+1, (long)stats->insertions[ilen], (long)stats->deletions[ilen]);
}
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,stats->ins_cycles[ilen],stats->del_cycles[ilen]);
+ printf("IC\t%d\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles[ilen], (long)stats->del_cycles[ilen]);
}
printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
- printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1,stats->cov[0]);
+ printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
int icov;
for (icov=1; icov<stats->ncov-1; icov++)
- printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1,stats->cov[icov]);
- printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov[stats->ncov-1]);
+ printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
+ printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
// Calculate average GC content, then sort by GC and depth
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;
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);
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);
projects / samtools.git / blobdiff