- coverage distribution ignores softclips and deletions
- some stats require sorted BAMs
- GC content graph can have an untidy, step-like pattern when BAM contains multiple read lengths.
- - The whole reads are used with -t, no splicing is done, no indels or soft clips are
- considered, even small overlap is good enough to include the read in the stats.
+ - 'bases mapped' (stats->nbases_mapped) is calculated from read lengths given by BAM (core.l_qseq)
+ - With the -t option, the whole reads are used. Except for the number of mapped bases (cigar)
+ counts, no splicing is done, no indels or soft clips are considered, even small overlap is
+ good enough to include the read in the stats.
+
*/
-#define BAMCHECK_VERSION "2012-04-04"
+#define BAMCHECK_VERSION "2012-04-24"
#define _ISOC99_SOURCE
#include <stdio.h>
{
// Parameters
int trim_qual; // bwa trim quality
- int rmdup; // Exclude reads marked as duplicates from the stats
// Dimensions of the quality histogram holder (quals_1st,quals_2nd), GC content holder (gc_1st,gc_2nd),
// insert size histogram holder
uint64_t *acgt_cycles;
uint64_t *read_lengths;
uint64_t *insertions, *deletions;
- uint64_t *ins_cycles, *del_cycles;
+ uint64_t *ins_cycles_1st, *ins_cycles_2nd, *del_cycles_1st, *del_cycles_2nd;
// The extremes encountered
int max_len; // Maximum read length
int filter_readlen;
// Target regions
- int nregions;
+ int nregions, reg_from,reg_to;
regions_t *regions;
// Auxiliary data
+ int flag_require, flag_filter;
double sum_qual; // For calculating average quality value
samfile_t *sam; // Unused
faidx_t *fai; // Reference sequence for GC-depth graph
stats_t;
void error(const char *format, ...);
+void bam_init_header_hash(bam_header_t *header);
+int is_in_regions(bam1_t *bam_line, stats_t *stats);
+
// Coverage distribution methods
inline int coverage_idx(int min, int max, int n, int step, int depth)
void count_indels(stats_t *stats,bam1_t *bam_line)
{
int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+ int is_1st = IS_READ1(bam_line) ? 1 : 0;
int icig;
int icycle = 0;
int read_len = bam_line->core.l_qseq;
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]++;
+ if ( is_1st )
+ stats->ins_cycles_1st[idx]++;
+ else
+ stats->ins_cycles_2nd[idx]++;
icycle += ncig;
if ( ncig<=stats->nindels )
stats->insertions[ncig-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 ( is_1st )
+ stats->del_cycles_1st[idx]++;
+ else
+ stats->del_cycles_2nd[idx]++;
if ( ncig<=stats->nindels )
stats->deletions[ncig-1]++;
continue;
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+1)*sizeof(uint64_t));
- if ( !stats->ins_cycles )
+ stats->ins_cycles_1st = realloc(stats->ins_cycles_1st, (n+1)*sizeof(uint64_t));
+ if ( !stats->ins_cycles_1st )
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));
+ memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
- stats->del_cycles = realloc(stats->del_cycles, (n+1)*sizeof(uint64_t));
- if ( !stats->del_cycles )
+ stats->ins_cycles_2nd = realloc(stats->ins_cycles_2nd, (n+1)*sizeof(uint64_t));
+ if ( !stats->ins_cycles_2nd )
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));
+ memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
+
+ stats->del_cycles_1st = realloc(stats->del_cycles_1st, (n+1)*sizeof(uint64_t));
+ if ( !stats->del_cycles_1st )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+ memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
+
+ stats->del_cycles_2nd = realloc(stats->del_cycles_2nd, (n+1)*sizeof(uint64_t));
+ if ( !stats->del_cycles_2nd )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,(n+1)*sizeof(uint64_t));
+ memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t));
stats->nbases = n;
void collect_stats(bam1_t *bam_line, stats_t *stats)
{
- if ( stats->rmdup && IS_DUP(bam_line) )
+ if ( stats->flag_require && (bam_line->core.flag & stats->flag_require)!=stats->flag_require )
+ return;
+ if ( stats->flag_filter && (bam_line->core.flag & stats->flag_filter) )
+ return;
+
+ if ( !is_in_regions(bam_line,stats) )
return;
int seq_len = bam_line->core.l_qseq;
stats->nmismatches += bam_aux2i(nm);
// Number of mapped bases from cigar
+ // Conversion from uint32_t to MIDNSHP
+ // 012-4--
+ // MIDNSHP
if ( bam_line->core.n_cigar == 0)
error("FIXME: mapped read with no cigar?\n");
- int readlen = seq_len;
- for (i=0; i<bam_line->core.n_cigar; i++)
+ int readlen=seq_len;
+ if ( stats->regions )
{
- // Conversion from uint32_t to MIDNSHP
- // 01--4--
- // MIDNSHP
- if ( (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==0 || (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==1 )
- stats->nbases_mapped_cigar += bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
-
- if ( (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==2 )
- readlen += bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
+ // Count only on-target bases
+ int iref = bam_line->core.pos + 1;
+ for (i=0; i<bam_line->core.n_cigar; i++)
+ {
+ int cig = bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK;
+ int ncig = bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
+ if ( cig==2 ) readlen += ncig;
+ else if ( cig==0 )
+ {
+ if ( iref < stats->reg_from ) ncig -= stats->reg_from-iref;
+ else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to;
+ if ( ncig<0 ) ncig = 0;
+ stats->nbases_mapped_cigar += ncig;
+ iref += bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
+ }
+ else if ( cig==1 )
+ {
+ iref += ncig;
+ if ( iref>=stats->reg_from && iref<=stats->reg_to )
+ stats->nbases_mapped_cigar += ncig;
+ }
+ }
+ }
+ else
+ {
+ // Count the whole read
+ for (i=0; i<bam_line->core.n_cigar; i++)
+ {
+ if ( (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==0 || (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==1 )
+ stats->nbases_mapped_cigar += bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
+ if ( (bam1_cigar(bam_line)[i]&BAM_CIGAR_MASK)==2 )
+ readlen += bam1_cigar(bam_line)[i]>>BAM_CIGAR_SHIFT;
+ }
}
stats->nbases_mapped += seq_len;
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");
+ printf("# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n");
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]);
+ if ( stats->ins_cycles_1st[ilen]>0 || stats->ins_cycles_2nd[ilen]>0 || stats->del_cycles_1st[ilen]>0 || stats->del_cycles_2nd[ilen]>0 )
+ printf("IC\t%d\t%ld\t%ld\t%ld\t%ld\n", ilen+1, (long)stats->ins_cycles_1st[ilen], (long)stats->ins_cycles_2nd[ilen], (long)stats->del_cycles_1st[ilen], (long)stats->del_cycles_2nd[ilen]);
}
printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
}
}
-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)
if ( iter == kh_end(header_hash) )
{
if ( !warned )
- fprintf(stderr,"Warning: Some sequences not present in the BAM (%s)\n", line);
+ fprintf(stderr,"Warning: Some sequences not present in the BAM, e.g. \"%s\". This message is printed only once.\n", line);
warned = 1;
continue;
}
stats->regions[tid].npos++;
}
if (line) free(line);
+ if ( !stats->regions ) error("Unable to map the -t sequences to the BAM sequences.\n");
fclose(fp);
}
return 1;
}
+void reset_regions(stats_t *stats)
+{
+ int i;
+ for (i=0; i<stats->nregions; i++)
+ stats->regions[i].cpos = 0;
+}
+
+int is_in_regions(bam1_t *bam_line, stats_t *stats)
+{
+ if ( !stats->regions ) return 1;
+
+ if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) return 0;
+ if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
+
+ regions_t *reg = &stats->regions[bam_line->core.tid];
+ if ( reg->cpos==reg->npos ) return 0; // done for this chr
+
+ // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered,
+ // even small overlap is enough to include the read in the stats.
+ int i = reg->cpos;
+ while ( i<reg->npos && reg->pos[i].to<=bam_line->core.pos ) i++;
+ if ( i>=reg->npos ) { reg->cpos = reg->npos; return 0; }
+ if ( bam_line->core.pos + bam_line->core.l_qseq + 1 < reg->pos[i].from ) return 0;
+ reg->cpos = i;
+ stats->reg_from = reg->pos[i].from;
+ stats->reg_to = reg->pos[i].to;
+
+ return 1;
+}
void error(const char *format, ...)
{
printf("Options:\n");
printf(" -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1]\n");
printf(" -d, --remove-dups Exlude from statistics reads marked as duplicates\n");
+ printf(" -f, --required-flag <int> Required flag, 0 for unset [0]\n");
+ printf(" -F, --filtering-flag <int> Filtering flag, 0 for unset [0]\n");
printf(" -h, --help This help message\n");
printf(" -i, --insert-size <int> Maximum insert size [8000]\n");
printf(" -l, --read-length <int> Include in the statistics only reads with the given read length []\n");
{"most-inserts",0,0,'m'},
{"trim-quality",0,0,'q'},
{"target-regions",0,0,'t'},
+ {"required-flag",0,0,'f'},
+ {"filtering-flag",0,0,'F'},
{0,0,0,0}
};
int opt;
- while ( (opt=getopt_long(argc,argv,"?hdsr:c:l:i:t:m:q:",loptions,NULL))>0 )
+ while ( (opt=getopt_long(argc,argv,"?hdsr:c:l:i:t:m:q:f:F:",loptions,NULL))>0 )
{
switch (opt)
{
- case 'd': stats->rmdup=1; break;
+ case 'f': stats->flag_require=strtol(optarg,0,0); break;
+ case 'F': stats->flag_filter=strtol(optarg,0,0); break;
+ case 'd': stats->flag_filter|=BAM_FDUP; break;
case 's': strcpy(in_mode, "r"); break;
case 'r': stats->fai = fai_load(optarg);
if (stats->fai==0)
stats->sam = sam;
bam1_t *bam_line = bam_init1();
// .. arrays
- stats->quals_1st = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
- stats->quals_2nd = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
- stats->gc_1st = calloc(stats->ngc,sizeof(uint64_t));
- stats->gc_2nd = calloc(stats->ngc,sizeof(uint64_t));
- stats->isize_inward = calloc(stats->nisize,sizeof(uint64_t));
- stats->isize_outward = calloc(stats->nisize,sizeof(uint64_t));
- stats->isize_other = calloc(stats->nisize,sizeof(uint64_t));
- stats->gcd = calloc(stats->ngcd,sizeof(gc_depth_t));
- stats->rseq_buf = calloc(stats->nref_seq,sizeof(uint8_t));
- stats->mpc_buf = stats->fai ? calloc(stats->nquals*stats->nbases,sizeof(uint64_t)) : NULL;
- stats->acgt_cycles = calloc(4*stats->nbases,sizeof(uint64_t));
- 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+1,sizeof(uint64_t));
- stats->del_cycles = calloc(stats->nbases+1,sizeof(uint64_t));
+ stats->quals_1st = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+ stats->quals_2nd = calloc(stats->nquals*stats->nbases,sizeof(uint64_t));
+ stats->gc_1st = calloc(stats->ngc,sizeof(uint64_t));
+ stats->gc_2nd = calloc(stats->ngc,sizeof(uint64_t));
+ stats->isize_inward = calloc(stats->nisize,sizeof(uint64_t));
+ stats->isize_outward = calloc(stats->nisize,sizeof(uint64_t));
+ stats->isize_other = calloc(stats->nisize,sizeof(uint64_t));
+ stats->gcd = calloc(stats->ngcd,sizeof(gc_depth_t));
+ stats->rseq_buf = calloc(stats->nref_seq,sizeof(uint8_t));
+ stats->mpc_buf = stats->fai ? calloc(stats->nquals*stats->nbases,sizeof(uint64_t)) : NULL;
+ stats->acgt_cycles = calloc(4*stats->nbases,sizeof(uint64_t));
+ 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_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+ stats->ins_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
+ stats->del_cycles_1st = calloc(stats->nbases+1,sizeof(uint64_t));
+ stats->del_cycles_2nd = calloc(stats->nbases+1,sizeof(uint64_t));
if ( targets )
init_regions(stats, targets);
int tid, beg, end;
bam_parse_region(stats->sam->header, argv[i], &tid, &beg, &end);
if ( tid < 0 ) continue;
+ reset_regions(stats);
bam_fetch(stats->sam->x.bam, bam_idx, tid, beg, end, stats, fetch_read);
}
bam_index_destroy(bam_idx);
{
// Stream through the entire BAM ignoring off-target regions if -t is given
while (samread(sam,bam_line) >= 0)
- {
- if ( stats->regions )
- {
- if ( bam_line->core.tid >= stats->nregions || bam_line->core.tid<0 ) continue;
- if ( !stats->is_sorted ) error("The BAM must be sorted in order for -t to work.\n");
-
- regions_t *reg = &stats->regions[bam_line->core.tid];
- if ( reg->cpos==reg->npos ) continue; // done for this chr
-
- // Find a matching interval or skip this read. No splicing of reads is done, no indels or soft clips considered,
- // even small overlap is enough to include the read in the stats.
- int i = reg->cpos;
- while ( i<reg->npos && reg->pos[i].to<=bam_line->core.pos ) i++;
- if ( i>=reg->npos ) { reg->cpos = reg->npos; continue; }
- if ( bam_line->core.pos + bam_line->core.l_qseq + 1 < reg->pos[i].from ) continue;
- reg->cpos = i;
- }
collect_stats(bam_line,stats);
- }
}
round_buffer_flush(stats,-1);
free(stats->read_lengths);
free(stats->insertions);
free(stats->deletions);
- free(stats->ins_cycles);
- free(stats->del_cycles);
+ free(stats->ins_cycles_1st);
+ free(stats->ins_cycles_2nd);
+ free(stats->del_cycles_1st);
+ free(stats->del_cycles_2nd);
destroy_regions(stats);
free(stats);
projects / samtools.git / blobdiff