--- /dev/null
- printf("SN\tsequences:\t%ld\n", stats->nreads_1st+stats->nreads_2nd);
+ /*
+ Author: petr.danecek@sanger
+ gcc -Wall -Winline -g -O2 -I ~/git/samtools bamcheck.c -o bamcheck -lm -lz -L ~/git/samtools -lbam
+
+ Assumptions, approximations and other issues:
+ - GC-depth graph does not split reads, the starting position determines which bin is incremented.
+ There are small overlaps between bins (max readlen-1). However, the bins are big (20k).
+ - 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.
+ */
+
+ #define BAMCHECK_VERSION "2012-03-29"
+
+ #define _ISOC99_SOURCE
+ #define _GNU_SOURCE
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <stdarg.h>
+ #include <string.h>
+ #include <math.h>
+ #include <ctype.h>
+ #include <getopt.h>
+ #include <errno.h>
+ #include "faidx.h"
+ #include "khash.h"
+ #include "sam.h"
+ #include "razf.h"
+
+ #define BWA_MIN_RDLEN 35
+ #define IS_PAIRED(bam) ((bam)->core.flag&BAM_FPAIRED && !((bam)->core.flag&BAM_FUNMAP) && !((bam)->core.flag&BAM_FMUNMAP))
+ #define IS_UNMAPPED(bam) ((bam)->core.flag&BAM_FUNMAP)
+ #define IS_REVERSE(bam) ((bam)->core.flag&BAM_FREVERSE)
+ #define IS_MATE_REVERSE(bam) ((bam)->core.flag&BAM_FMREVERSE)
+ #define IS_READ1(bam) ((bam)->core.flag&BAM_FREAD1)
+ #define IS_READ2(bam) ((bam)->core.flag&BAM_FREAD2)
+ #define IS_DUP(bam) ((bam)->core.flag&BAM_FDUP)
+
+ typedef struct
+ {
+ int32_t line_len, line_blen;
+ int64_t len;
+ uint64_t offset;
+ }
+ faidx1_t;
+ KHASH_MAP_INIT_STR(s, faidx1_t)
+ KHASH_MAP_INIT_STR(str, int)
+ struct __faidx_t {
+ RAZF *rz;
+ int n, m;
+ char **name;
+ khash_t(s) *hash;
+ };
+
+ typedef struct
+ {
+ float gc;
+ uint32_t depth;
+ }
+ gc_depth_t;
+
+ // For coverage distribution, a simple pileup
+ typedef struct
+ {
+ int64_t pos;
+ int size, start;
+ int *buffer;
+ }
+ round_buffer_t;
+
+ typedef struct { uint32_t from, to; } pos_t;
+ typedef struct
+ {
+ int npos,mpos,cpos;
+ pos_t *pos;
+ }
+ regions_t;
+
+ typedef struct
+ {
+ // 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
+ int nquals; // The number of quality bins
+ int nbases; // The maximum sequence length the allocated array can hold
+ int nisize; // The maximum insert size that the allocated array can hold
+ int ngc; // The size of gc_1st and gc_2nd
+ int nindels; // The maximum indel length for indel distribution
+
+ // Arrays for the histogram data
+ uint64_t *quals_1st, *quals_2nd;
+ uint64_t *gc_1st, *gc_2nd;
+ uint64_t *isize_inward, *isize_outward, *isize_other;
+ uint64_t *acgt_cycles;
+ uint64_t *read_lengths;
+ uint64_t *insertions, *deletions;
+ uint64_t *ins_cycles, *del_cycles;
+
+ // The extremes encountered
+ int max_len; // Maximum read length
+ int max_qual; // Maximum quality
+ float isize_main_bulk; // There are always some unrealistically big insert sizes, report only the main part
+ int is_sorted;
+
+ // Summary numbers
+ uint64_t total_len;
+ uint64_t total_len_dup;
+ uint64_t nreads_1st;
+ uint64_t nreads_2nd;
+ uint64_t nreads_dup;
+ uint64_t nreads_unmapped;
+ uint64_t nreads_unpaired;
+ uint64_t nreads_paired;
+ uint64_t nreads_mq0;
+ uint64_t nbases_mapped;
+ uint64_t nbases_mapped_cigar;
+ uint64_t nbases_trimmed; // bwa trimmed bases
+ uint64_t nmismatches;
+
+ // GC-depth related data
+ uint32_t ngcd, igcd; // The maximum number of GC depth bins and index of the current bin
+ gc_depth_t *gcd; // The GC-depth bins holder
+ int gcd_bin_size; // The size of GC-depth bin
+ int32_t tid, gcd_pos; // Position of the current bin
+ int32_t pos; // Position of the last read
+
+ // Coverage distribution related data
+ int ncov; // The number of coverage bins
+ uint64_t *cov; // The coverage frequencies
+ int cov_min,cov_max,cov_step; // Minimum, maximum coverage and size of the coverage bins
+ round_buffer_t cov_rbuf; // Pileup round buffer
+
+ // Mismatches by read cycle
+ uint8_t *rseq_buf; // A buffer for reference sequence to check the mismatches against
+ int nref_seq; // The size of the buffer
+ int32_t rseq_pos; // The coordinate of the first base in the buffer
+ int32_t rseq_len; // The used part of the buffer
+ uint64_t *mpc_buf; // Mismatches per cycle
+
+ // Filters
+ int filter_readlen;
+
+ // Target regions
+ int nregions;
+ regions_t *regions;
+
+ // Auxiliary data
+ double sum_qual; // For calculating average quality value
+ samfile_t *sam; // Unused
+ faidx_t *fai; // Reference sequence for GC-depth graph
+ int argc; // Command line arguments to be printed on the output
+ char **argv;
+ }
+ stats_t;
+
+ void error(const char *format, ...);
+
+ // Coverage distribution methods
+ inline int coverage_idx(int min, int max, int n, int step, int depth)
+ {
+ if ( depth < min )
+ return 0;
+
+ if ( depth > max )
+ return n-1;
+
+ return 1 + (depth - min) / step;
+ }
+
+ inline int round_buffer_lidx2ridx(int offset, int size, int64_t refpos, int64_t pos)
+ {
+ return (offset + (pos-refpos) % size) % size;
+ }
+
+ void round_buffer_flush(stats_t *stats, int64_t pos)
+ {
+ int ibuf,idp;
+
+ if ( pos==stats->cov_rbuf.pos )
+ return;
+
+ int64_t new_pos = pos;
+ if ( pos==-1 || pos - stats->cov_rbuf.pos >= stats->cov_rbuf.size )
+ {
+ // Flush the whole buffer, but in sequential order,
+ pos = stats->cov_rbuf.pos + stats->cov_rbuf.size - 1;
+ }
+
+ if ( pos < stats->cov_rbuf.pos )
+ error("Expected coordinates in ascending order, got %ld after %ld\n", pos,stats->cov_rbuf.pos);
+
+ int ifrom = stats->cov_rbuf.start;
+ int ito = round_buffer_lidx2ridx(stats->cov_rbuf.start,stats->cov_rbuf.size,stats->cov_rbuf.pos,pos-1);
+ if ( ifrom>ito )
+ {
+ for (ibuf=ifrom; ibuf<stats->cov_rbuf.size; ibuf++)
+ {
+ if ( !stats->cov_rbuf.buffer[ibuf] )
+ continue;
+ idp = coverage_idx(stats->cov_min,stats->cov_max,stats->ncov,stats->cov_step,stats->cov_rbuf.buffer[ibuf]);
+ stats->cov[idp]++;
+ stats->cov_rbuf.buffer[ibuf] = 0;
+ }
+ ifrom = 0;
+ }
+ for (ibuf=ifrom; ibuf<=ito; ibuf++)
+ {
+ if ( !stats->cov_rbuf.buffer[ibuf] )
+ continue;
+ idp = coverage_idx(stats->cov_min,stats->cov_max,stats->ncov,stats->cov_step,stats->cov_rbuf.buffer[ibuf]);
+ stats->cov[idp]++;
+ stats->cov_rbuf.buffer[ibuf] = 0;
+ }
+ stats->cov_rbuf.start = (new_pos==-1) ? 0 : round_buffer_lidx2ridx(stats->cov_rbuf.start,stats->cov_rbuf.size,stats->cov_rbuf.pos,pos);
+ stats->cov_rbuf.pos = new_pos;
+ }
+
+ void round_buffer_insert_read(round_buffer_t *rbuf, int64_t from, int64_t to)
+ {
+ if ( to-from >= rbuf->size )
+ error("The read length too big (%d), please increase the buffer length (currently %d)\n", to-from+1,rbuf->size);
+ if ( from < rbuf->pos )
+ error("The reads are not sorted (%ld comes after %ld).\n", from,rbuf->pos);
+
+ int ifrom,ito,ibuf;
+ ifrom = round_buffer_lidx2ridx(rbuf->start,rbuf->size,rbuf->pos,from);
+ ito = round_buffer_lidx2ridx(rbuf->start,rbuf->size,rbuf->pos,to);
+ if ( ifrom>ito )
+ {
+ for (ibuf=ifrom; ibuf<rbuf->size; ibuf++)
+ rbuf->buffer[ibuf]++;
+ ifrom = 0;
+ }
+ for (ibuf=ifrom; ibuf<=ito; ibuf++)
+ rbuf->buffer[ibuf]++;
+ }
+
+ // Calculate the number of bases in the read trimmed by BWA
+ int bwa_trim_read(int trim_qual, uint8_t *quals, int len, int reverse)
+ {
+ if ( len<BWA_MIN_RDLEN ) return 0;
+
+ // Although the name implies that the read cannot be trimmed to more than BWA_MIN_RDLEN,
+ // the calculation can in fact trim it to (BWA_MIN_RDLEN-1). (bwa_trim_read in bwa/bwaseqio.c).
+ int max_trimmed = len - BWA_MIN_RDLEN + 1;
+ int l, sum=0, max_sum=0, max_l=0;
+
+ for (l=0; l<max_trimmed; l++)
+ {
+ sum += trim_qual - quals[ reverse ? l : len-1-l ];
+ if ( sum<0 ) break;
+ if ( sum>max_sum )
+ {
+ max_sum = sum;
+ // This is the correct way, but bwa clips from some reason one base less
+ // max_l = l+1;
+ max_l = l;
+ }
+ }
+ return max_l;
+ }
+
+
+ void count_indels(stats_t *stats,bam1_t *bam_line)
+ {
+ int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+ int icig;
+ int icycle = 0;
+ int read_len = bam_line->core.l_qseq;
+ for (icig=0; icig<bam_line->core.n_cigar; icig++)
+ {
+ // Conversion from uint32_t to MIDNSHP
+ // 0123456
+ // MIDNSHP
+ int cig = bam1_cigar(bam_line)[icig] & BAM_CIGAR_MASK;
+ int ncig = bam1_cigar(bam_line)[icig] >> BAM_CIGAR_SHIFT;
+
+ 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);
+ stats->ins_cycles[idx]++;
+ icycle += ncig;
+ if ( ncig<=stats->nindels )
+ stats->insertions[ncig-1]++;
+ continue;
+ }
+ if ( cig==2 )
+ {
+ int idx = is_fwd ? icycle : read_len-icycle-1;
+ if ( idx >= stats->nbases ) error("FIXME: %d vs %d\n", idx,stats->nbases);
+ stats->del_cycles[idx]++;
+ if ( ncig<=stats->nindels )
+ stats->deletions[ncig-1]++;
+ continue;
+ }
+ icycle += ncig;
+ }
+ }
+
+ void count_mismatches_per_cycle(stats_t *stats,bam1_t *bam_line)
+ {
+ int is_fwd = IS_REVERSE(bam_line) ? 0 : 1;
+ int icig,iread=0,icycle=0;
+ int iref = bam_line->core.pos - stats->rseq_pos;
+ int read_len = bam_line->core.l_qseq;
+ uint8_t *read = bam1_seq(bam_line);
+ uint8_t *quals = bam1_qual(bam_line);
+ uint64_t *mpc_buf = stats->mpc_buf;
+ for (icig=0; icig<bam_line->core.n_cigar; icig++)
+ {
+ // Conversion from uint32_t to MIDNSHP
+ // 0123456
+ // MIDNSHP
+ int cig = bam1_cigar(bam_line)[icig] & BAM_CIGAR_MASK;
+ int ncig = bam1_cigar(bam_line)[icig] >> BAM_CIGAR_SHIFT;
+ if ( cig==1 )
+ {
+ iread += ncig;
+ icycle += ncig;
+ continue;
+ }
+ if ( cig==2 )
+ {
+ iref += ncig;
+ continue;
+ }
+ if ( cig==4 )
+ {
+ icycle += ncig;
+ // Soft-clips are present in the sequence, but the position of the read marks a start of non-clipped sequence
+ // iref += ncig;
+ iread += ncig;
+ continue;
+ }
+ if ( cig==5 )
+ {
+ icycle += ncig;
+ continue;
+ }
+ if ( cig!=0 )
+ error("TODO: cigar %d, %s\n", cig,bam1_qname(bam_line));
+
+ if ( ncig+iref > stats->rseq_len )
+ error("FIXME: %d+%d > %d, %s, %s:%d\n",ncig,iref,stats->rseq_len, bam1_qname(bam_line),stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1);
+
+ int im;
+ for (im=0; im<ncig; im++)
+ {
+ uint8_t cread = bam1_seqi(read,iread);
+ uint8_t cref = stats->rseq_buf[iref];
+
+ // ---------------15
+ // =ACMGRSVTWYHKDBN
+ if ( cread==15 )
+ {
+ int idx = is_fwd ? icycle : read_len-icycle-1;
+ if ( idx>stats->max_len )
+ error("mpc: %d>%d\n",idx,stats->max_len);
+ idx = idx*stats->nquals;
+ if ( idx>=stats->nquals*stats->nbases )
+ error("FIXME: mpc_buf overflow\n");
+ mpc_buf[idx]++;
+ }
+ else if ( cref && cread && cref!=cread )
+ {
+ uint8_t qual = quals[iread] + 1;
+ if ( qual>=stats->nquals )
+ error("TODO: quality too high %d>=%d\n", quals[iread],stats->nquals);
+
+ int idx = is_fwd ? icycle : read_len-icycle-1;
+ if ( idx>stats->max_len )
+ error("mpc: %d>%d\n",idx,stats->max_len);
+
+ idx = idx*stats->nquals + qual;
+ if ( idx>=stats->nquals*stats->nbases )
+ error("FIXME: mpc_buf overflow\n");
+ mpc_buf[idx]++;
+ }
+
+ iref++;
+ iread++;
+ icycle++;
+ }
+ }
+ }
+
+ void read_ref_seq(stats_t *stats,int32_t tid,int32_t pos)
+ {
+ khash_t(s) *h;
+ khiter_t iter;
+ faidx1_t val;
+ char *chr, c;
+ faidx_t *fai = stats->fai;
+
+ h = fai->hash;
+ chr = stats->sam->header->target_name[tid];
+
+ // ID of the sequence name
+ iter = kh_get(s, h, chr);
+ if (iter == kh_end(h))
+ error("No such reference sequence [%s]?\n", chr);
+ val = kh_value(h, iter);
+
+ // Check the boundaries
+ if (pos >= val.len)
+ error("Was the bam file mapped with the reference sequence supplied?"
+ " A read mapped beyond the end of the chromosome (%s:%d, chromosome length %d).\n", chr,pos,val.len);
+ int size = stats->nref_seq;
+ // The buffer extends beyond the chromosome end. Later the rest will be filled with N's.
+ if (size+pos > val.len) size = val.len-pos;
+
+ // Position the razf reader
+ razf_seek(fai->rz, val.offset + pos / val.line_blen * val.line_len + pos % val.line_blen, SEEK_SET);
+
+ uint8_t *ptr = stats->rseq_buf;
+ int nread = 0;
+ while ( nread<size && razf_read(fai->rz,&c,1) && !fai->rz->z_err )
+ {
+ if ( !isgraph(c) )
+ continue;
+
+ // Conversion between uint8_t coding and ACGT
+ // -12-4---8-------
+ // =ACMGRSVTWYHKDBN
+ if ( c=='A' || c=='a' )
+ *ptr = 1;
+ else if ( c=='C' || c=='c' )
+ *ptr = 2;
+ else if ( c=='G' || c=='g' )
+ *ptr = 4;
+ else if ( c=='T' || c=='t' )
+ *ptr = 8;
+ else
+ *ptr = 0;
+ ptr++;
+ nread++;
+ }
+ if ( nread < stats->nref_seq )
+ {
+ memset(ptr,0, stats->nref_seq - nread);
+ nread = stats->nref_seq;
+ }
+ stats->rseq_len = nread;
+ stats->rseq_pos = pos;
+ stats->tid = tid;
+ }
+
+ float fai_gc_content(stats_t *stats)
+ {
+ uint32_t gc,count,c;
+ int i,size = stats->rseq_len;
+
+ // Count GC content
+ gc = count = 0;
+ for (i=0; i<size; i++)
+ {
+ c = stats->rseq_buf[i];
+ if ( c==2 || c==4 )
+ {
+ gc++;
+ count++;
+ }
+ else if ( c==1 || c==8 )
+ count++;
+ }
+ return count ? (float)gc/count : 0;
+ }
+
+
+ void realloc_buffers(stats_t *stats, int seq_len)
+ {
+ int n = 2*(1 + seq_len - stats->nbases) + stats->nbases;
+
+ stats->quals_1st = realloc(stats->quals_1st, n*stats->nquals*sizeof(uint64_t));
+ if ( !stats->quals_1st )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+ memset(stats->quals_1st + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+ stats->quals_2nd = realloc(stats->quals_2nd, n*stats->nquals*sizeof(uint64_t));
+ if ( !stats->quals_2nd )
+ error("Could not realloc buffers, the sequence too long: %d (2x%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+ memset(stats->quals_2nd + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+
+ if ( stats->mpc_buf )
+ {
+ stats->mpc_buf = realloc(stats->mpc_buf, n*stats->nquals*sizeof(uint64_t));
+ if ( !stats->mpc_buf )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*stats->nquals*sizeof(uint64_t));
+ memset(stats->mpc_buf + stats->nbases*stats->nquals, 0, (n-stats->nbases)*stats->nquals*sizeof(uint64_t));
+ }
+
+ stats->acgt_cycles = realloc(stats->acgt_cycles, n*4*sizeof(uint64_t));
+ if ( !stats->acgt_cycles )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*4*sizeof(uint64_t));
+ memset(stats->acgt_cycles + stats->nbases*4, 0, (n-stats->nbases)*4*sizeof(uint64_t));
+
+ stats->read_lengths = realloc(stats->read_lengths, n*sizeof(uint64_t));
+ if ( !stats->read_lengths )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+ memset(stats->read_lengths + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+ stats->insertions = realloc(stats->insertions, n*sizeof(uint64_t));
+ if ( !stats->insertions )
+ error("Could not realloc buffers, the sequence too long: %d (%ld)\n", seq_len,n*sizeof(uint64_t));
+ memset(stats->insertions + stats->nbases, 0, (n-stats->nbases)*sizeof(uint64_t));
+
+ stats->deletions = realloc(stats->deletions, n*sizeof(uint64_t));
+ if ( !stats->deletions )
+ 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));
+ 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));
+
+ stats->del_cycles = realloc(stats->del_cycles, n*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));
+
+ stats->nbases = n;
+
+ // Realloc the coverage distribution buffer
+ int *rbuffer = calloc(sizeof(int),seq_len*5);
+ n = stats->cov_rbuf.size-stats->cov_rbuf.start;
+ memcpy(rbuffer,stats->cov_rbuf.buffer+stats->cov_rbuf.start,n);
+ if ( stats->cov_rbuf.start>1 )
+ memcpy(rbuffer+n,stats->cov_rbuf.buffer,stats->cov_rbuf.start);
+ stats->cov_rbuf.start = 0;
+ free(stats->cov_rbuf.buffer);
+ stats->cov_rbuf.buffer = rbuffer;
+ stats->cov_rbuf.size = seq_len*5;
+ }
+
+ void collect_stats(bam1_t *bam_line, stats_t *stats)
+ {
+ if ( stats->rmdup && IS_DUP(bam_line) )
+ return;
+
+ int seq_len = bam_line->core.l_qseq;
+ if ( !seq_len ) return;
+ if ( stats->filter_readlen!=-1 && seq_len!=stats->filter_readlen ) return;
+ if ( seq_len >= stats->nbases )
+ realloc_buffers(stats,seq_len);
+ if ( stats->max_len<seq_len )
+ stats->max_len = seq_len;
+
+ stats->read_lengths[seq_len]++;
+
+ // Count GC and ACGT per cycle
+ uint8_t base, *seq = bam1_seq(bam_line);
+ int gc_count = 0;
+ int i;
+ int reverse = IS_REVERSE(bam_line);
+ for (i=0; i<seq_len; i++)
+ {
+ // Conversion from uint8_t coding to ACGT
+ // -12-4---8-------
+ // =ACMGRSVTWYHKDBN
+ // 01 2 3
+ base = bam1_seqi(seq,i);
+ base /= 2;
+ if ( base==1 || base==2 ) gc_count++;
+ else if ( base>2 ) base=3;
+ if ( 4*(reverse ? seq_len-i-1 : i) + base >= stats->nbases*4 )
+ error("FIXME: acgt_cycles\n");
+ stats->acgt_cycles[ 4*(reverse ? seq_len-i-1 : i) + base ]++;
+ }
+ int gc_idx_min = gc_count*(stats->ngc-1)/seq_len;
+ int gc_idx_max = (gc_count+1)*(stats->ngc-1)/seq_len;
+ if ( gc_idx_max >= stats->ngc ) gc_idx_max = stats->ngc - 1;
+
+ // Determine which array (1st or 2nd read) will these stats go to,
+ // trim low quality bases from end the same way BWA does,
+ // fill GC histogram
+ uint64_t *quals;
+ uint8_t *bam_quals = bam1_qual(bam_line);
+ if ( bam_line->core.flag&BAM_FREAD2 )
+ {
+ quals = stats->quals_2nd;
+ stats->nreads_2nd++;
+ for (i=gc_idx_min; i<gc_idx_max; i++)
+ stats->gc_2nd[i]++;
+ }
+ else
+ {
+ quals = stats->quals_1st;
+ stats->nreads_1st++;
+ for (i=gc_idx_min; i<gc_idx_max; i++)
+ stats->gc_1st[i]++;
+ }
+ if ( stats->trim_qual>0 )
+ stats->nbases_trimmed += bwa_trim_read(stats->trim_qual, bam_quals, seq_len, reverse);
+
+ // Quality histogram and average quality
+ for (i=0; i<seq_len; i++)
+ {
+ uint8_t qual = bam_quals[ reverse ? seq_len-i-1 : i];
+ if ( qual>=stats->nquals )
+ error("TODO: quality too high %d>=%d\n", quals[i],stats->nquals);
+ if ( qual>stats->max_qual )
+ stats->max_qual = qual;
+
+ quals[ i*stats->nquals+qual ]++;
+ stats->sum_qual += qual;
+ }
+
+ // Look at the flags and increment appropriate counters (mapped, paired, etc)
+ if ( IS_UNMAPPED(bam_line) )
+ stats->nreads_unmapped++;
+ else
+ {
+ if ( !bam_line->core.qual )
+ stats->nreads_mq0++;
+
+ count_indels(stats,bam_line);
+
+ // The insert size is tricky, because for long inserts the libraries are
+ // prepared differently and the pairs point in other direction. BWA does
+ // not set the paired flag for them. Similar thing is true also for 454
+ // reads. Therefore, do the insert size stats for all mapped reads.
+ int32_t isize = bam_line->core.isize;
+ if ( isize<0 ) isize = -isize;
+ if ( IS_PAIRED(bam_line) && isize!=0 )
+ {
+ stats->nreads_paired++;
+ if ( isize >= stats->nisize )
+ isize=stats->nisize-1;
+
+ int pos_fst = bam_line->core.mpos - bam_line->core.pos;
+ int is_fst = IS_READ1(bam_line) ? 1 : -1;
+ int is_fwd = IS_REVERSE(bam_line) ? -1 : 1;
+ int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+
+ if ( is_fwd*is_mfwd>0 )
+ stats->isize_other[isize]++;
+ else if ( is_fst*pos_fst>0 )
+ {
+ if ( is_fst*is_fwd>0 )
+ stats->isize_inward[isize]++;
+ else
+ stats->isize_outward[isize]++;
+ }
+ else if ( is_fst*pos_fst<0 )
+ {
+ if ( is_fst*is_fwd>0 )
+ stats->isize_outward[isize]++;
+ else
+ stats->isize_inward[isize]++;
+ }
+ }
+ else
+ stats->nreads_unpaired++;
+
+ // Number of mismatches
+ uint8_t *nm = bam_aux_get(bam_line,"NM");
+ if (nm)
+ stats->nmismatches += bam_aux2i(nm);
+
+ // Number of mapped bases from cigar
+ 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++)
+ {
+ // 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;
+ }
+ stats->nbases_mapped += seq_len;
+
+ if ( stats->tid==bam_line->core.tid && bam_line->core.pos<stats->pos )
+ stats->is_sorted = 0;
+ stats->pos = bam_line->core.pos;
+
+ if ( stats->is_sorted )
+ {
+ if ( stats->tid==-1 || stats->tid!=bam_line->core.tid )
+ round_buffer_flush(stats,-1);
+
+ // Mismatches per cycle and GC-depth graph
+ if ( stats->fai )
+ {
+ // First pass, new chromosome or sequence spanning beyond the end of the buffer
+ if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid || stats->rseq_pos+stats->rseq_len < bam_line->core.pos+readlen )
+ {
+ read_ref_seq(stats,bam_line->core.tid,bam_line->core.pos);
+
+ // Get the reference GC content for this bin. Note that in the current implementation
+ // the GCD bins overlap by seq_len-1. Because the bin size is by default 20k and the
+ // expected read length only ~100bp, it shouldn't really matter.
+ stats->gcd_pos = bam_line->core.pos;
+ stats->igcd++;
+
+ if ( stats->igcd >= stats->ngcd )
+ error("The genome too long or the GCD bin overlaps too big [%ud]\n", stats->igcd);
+
+ stats->gcd[ stats->igcd ].gc = fai_gc_content(stats);
+ }
+ count_mismatches_per_cycle(stats,bam_line);
+ }
+ else if ( stats->gcd_pos==-1 || stats->tid != bam_line->core.tid || bam_line->core.pos - stats->gcd_pos > stats->gcd_bin_size )
+ {
+ // First pass or a new chromosome
+ stats->tid = bam_line->core.tid;
+ stats->gcd_pos = bam_line->core.pos;
+ stats->igcd++;
+
+ if ( stats->igcd >= stats->ngcd )
+ {
+ uint32_t n = 2*(1 + stats->ngcd);
+ stats->gcd = realloc(stats->gcd, n*sizeof(gc_depth_t));
+ if ( !stats->gcd )
+ error("Could not realloc GCD buffer, too many chromosomes or the genome too long?? [%u %u]\n", stats->ngcd,n);
+ memset(&(stats->gcd[stats->ngcd]),0,(n-stats->ngcd)*sizeof(gc_depth_t));
+ }
+ }
+
+ stats->gcd[ stats->igcd ].depth++;
+ // When no reference sequence is given, approximate the GC from the read (much shorter window, but otherwise OK)
+ if ( !stats->fai )
+ stats->gcd[ stats->igcd ].gc += (float) gc_count / seq_len;
+
+ // Coverage distribution graph
+ round_buffer_flush(stats,bam_line->core.pos);
+ round_buffer_insert_read(&(stats->cov_rbuf),bam_line->core.pos,bam_line->core.pos+seq_len-1);
+ }
+ }
+
+ stats->total_len += seq_len;
+ if ( IS_DUP(bam_line) )
+ {
+ stats->total_len_dup += seq_len;
+ stats->nreads_dup++;
+ }
+ }
+
+ // Sort by GC and depth
+ #define GCD_t(x) ((gc_depth_t *)x)
+ static int gcd_cmp(const void *a, const void *b)
+ {
+ if ( GCD_t(a)->gc < GCD_t(b)->gc ) return -1;
+ if ( GCD_t(a)->gc > GCD_t(b)->gc ) return 1;
+ if ( GCD_t(a)->depth < GCD_t(b)->depth ) return -1;
+ if ( GCD_t(a)->depth > GCD_t(b)->depth ) return 1;
+ return 0;
+ }
+ #undef GCD_t
+
+ float gcd_percentile(gc_depth_t *gcd, int N, int p)
+ {
+ float n,d;
+ int k;
+
+ n = p*(N+1)/100;
+ k = n;
+ if ( k<=0 )
+ return gcd[0].depth;
+ if ( k>=N )
+ return gcd[N-1].depth;
+
+ d = n - k;
+ return gcd[k-1].depth + d*(gcd[k].depth - gcd[k-1].depth);
+ }
+
+ void output_stats(stats_t *stats)
+ {
+ // Calculate average insert size and standard deviation (from the main bulk data only)
+ int isize, ibulk=0;
+ uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0;
+ for (isize=1; isize<stats->nisize; isize++)
+ {
+ // Each pair was counted twice
+ stats->isize_inward[isize] *= 0.5;
+ stats->isize_outward[isize] *= 0.5;
+ stats->isize_other[isize] *= 0.5;
+
+ nisize_inward += stats->isize_inward[isize];
+ nisize_outward += stats->isize_outward[isize];
+ nisize_other += stats->isize_other[isize];
+ nisize += stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize];
+ }
+
+ double bulk=0, avg_isize=0, sd_isize=0;
+ for (isize=1; isize<stats->nisize; isize++)
+ {
+ bulk += stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize];
+ avg_isize += isize * (stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize]);
+
+ if ( bulk/nisize > stats->isize_main_bulk )
+ {
+ ibulk = isize+1;
+ nisize = bulk;
+ break;
+ }
+ }
+ avg_isize /= nisize ? nisize : 1;
+ for (isize=1; isize<ibulk; isize++)
+ sd_isize += (stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize]) * (isize-avg_isize)*(isize-avg_isize) / nisize;
+ sd_isize = sqrt(sd_isize);
+
+
+ printf("# This file was produced by bamcheck (%s)\n",BAMCHECK_VERSION);
+ printf("# The command line was: %s",stats->argv[0]);
+ int i;
+ for (i=1; i<stats->argc; i++)
+ printf(" %s",stats->argv[i]);
+ printf("\n");
+ printf("# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
- 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\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\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\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\tmaximum length:\t%d\n", stats->max_len);
+ 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("\t%ld", stats->quals_1st[ibase*stats->nquals+iqual]);
++ 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++;
+ if ( stats->max_qual+1<stats->nquals ) stats->max_qual++;
+ printf("# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n");
+ printf("# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+ for (ibase=0; ibase<stats->max_len; ibase++)
+ {
+ printf("FFQ\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_1st[ibase*stats->nquals+iqual]);
+ }
+ printf("\n");
+ }
+ printf("# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part.\n");
+ printf("# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n");
+ for (ibase=0; ibase<stats->max_len; ibase++)
+ {
+ printf("LFQ\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->quals_2nd[ibase*stats->nquals+iqual]);
+ }
+ printf("\n");
+ }
+ if ( stats->mpc_buf )
+ {
+ printf("# Mismatches per cycle and quality. Use `grep ^MPC | cut -f 2-` to extract this part.\n");
+ printf("# Columns correspond to qualities, rows to cycles. First column is the cycle number, second\n");
+ printf("# is the number of N's and the rest is the number of mismatches\n");
+ for (ibase=0; ibase<stats->max_len; ibase++)
+ {
+ printf("MPC\t%d",ibase+1);
+ for (iqual=0; iqual<=stats->max_qual; iqual++)
+ {
- printf("GCF\t%.2f\t%ld\n", (ibase+ibase_prev)*0.5*100./(stats->ngc-1),stats->gc_1st[ibase_prev]);
++ printf("\t%ld", (long)stats->mpc_buf[ibase*stats->nquals+iqual]);
+ }
+ printf("\n");
+ }
+ }
+ printf("# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.\n");
+ int ibase_prev = 0;
+ for (ibase=0; ibase<stats->ngc; ibase++)
+ {
+ if ( stats->gc_1st[ibase]==stats->gc_1st[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("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");
+ ibase_prev = 0;
+ for (ibase=0; ibase<stats->ngc; ibase++)
+ {
+ if ( stats->gc_2nd[ibase]==stats->gc_2nd[ibase_prev] ) continue;
- 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("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");
+ for (ibase=0; ibase<stats->max_len; ibase++)
+ {
+ uint64_t *ptr = &(stats->acgt_cycles[ibase*4]);
+ uint64_t sum = ptr[0]+ptr[1]+ptr[2]+ptr[3];
+ if ( ! sum ) continue;
+ printf("GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase,100.*ptr[0]/sum,100.*ptr[1]/sum,100.*ptr[2]/sum,100.*ptr[3]/sum);
+ }
+ 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("RL\t%d\t%ld\n", ilen,stats->read_lengths[ilen]);
++ 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("ID\t%d\t%ld\t%ld\n", ilen+1,stats->insertions[ilen],stats->deletions[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("IC\t%d\t%ld\t%ld\n", ilen+1,stats->ins_cycles[ilen],stats->del_cycles[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++)
+ {
+ if ( stats->ins_cycles[ilen]>0 || stats->del_cycles[ilen]>0 )
- printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1,stats->cov[0]);
++ 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-%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]\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, (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
+ printf("# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");
+ uint32_t igcd;
+ for (igcd=0; igcd<stats->igcd; igcd++)
+ {
+ if ( stats->fai )
+ stats->gcd[igcd].gc = round(100. * stats->gcd[igcd].gc);
+ else
+ if ( stats->gcd[igcd].depth )
+ stats->gcd[igcd].gc = round(100. * stats->gcd[igcd].gc / stats->gcd[igcd].depth);
+ }
+ qsort(stats->gcd, stats->igcd+1, sizeof(gc_depth_t), gcd_cmp);
+ igcd = 0;
+ while ( igcd < stats->igcd )
+ {
+ // Calculate percentiles (10,25,50,75,90th) for the current GC content and print
+ uint32_t nbins=0, itmp=igcd;
+ float gc = stats->gcd[igcd].gc;
+ while ( itmp<stats->igcd && fabs(stats->gcd[itmp].gc-gc)<0.1 )
+ {
+ nbins++;
+ itmp++;
+ }
+ printf("GCD\t%.1f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\n", gc, (igcd+nbins+1)*100./(stats->igcd+1),
+ gcd_percentile(&(stats->gcd[igcd]),nbins,10) *avg_read_length/stats->gcd_bin_size,
+ gcd_percentile(&(stats->gcd[igcd]),nbins,25) *avg_read_length/stats->gcd_bin_size,
+ gcd_percentile(&(stats->gcd[igcd]),nbins,50) *avg_read_length/stats->gcd_bin_size,
+ gcd_percentile(&(stats->gcd[igcd]),nbins,75) *avg_read_length/stats->gcd_bin_size,
+ gcd_percentile(&(stats->gcd[igcd]),nbins,90) *avg_read_length/stats->gcd_bin_size
+ );
+ igcd += nbins;
+ }
+ }
+
+ void bam_init_header_hash(bam_header_t *header);
+
+ void init_regions(stats_t *stats, char *file)
+ {
+ khiter_t iter;
+ khash_t(str) *header_hash;
+
+ bam_init_header_hash(stats->sam->header);
+ header_hash = (khash_t(str)*)stats->sam->header->hash;
+
+ FILE *fp = fopen(file,"r");
+ if ( !fp ) error("%s: %s\n",file,strerror(errno));
+
+ char *line = NULL;
+ size_t len = 0;
+ ssize_t nread;
+ int warned = 0;
+ int prev_tid=-1, prev_pos=-1;
+ while ((nread = getline(&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);
+ line[i] = 0;
+
+ iter = kh_get(str, header_hash, line);
+ int tid = kh_val(header_hash, iter);
+ if ( iter == kh_end(header_hash) )
+ {
+ if ( !warned )
+ fprintf(stderr,"Warning: Some sequences not present in the BAM (%s)\n", line);
+ warned = 1;
+ continue;
+ }
+
+ if ( tid >= stats->nregions )
+ {
+ stats->regions = realloc(stats->regions,sizeof(regions_t)*(stats->nregions+100));
+ int j;
+ for (j=stats->nregions; j<stats->nregions+100; j++)
+ {
+ stats->regions[j].npos = stats->regions[j].mpos = stats->regions[j].cpos = 0;
+ stats->regions[j].pos = NULL;
+ }
+ stats->nregions += 100;
+ }
+ int npos = stats->regions[tid].npos;
+ if ( npos >= stats->regions[tid].mpos )
+ {
+ stats->regions[tid].mpos += 1000;
+ stats->regions[tid].pos = realloc(stats->regions[tid].pos,sizeof(pos_t)*stats->regions[tid].mpos);
+ }
+
+ if ( (sscanf(line+i+1,"%d %d",&stats->regions[tid].pos[npos].from,&stats->regions[tid].pos[npos].to))!=2 ) error("Could not parse the region [%s]\n");
+ if ( prev_tid==-1 || prev_tid!=tid )
+ {
+ prev_tid = tid;
+ prev_pos = stats->regions[tid].pos[npos].from;
+ }
+ if ( prev_pos>stats->regions[tid].pos[npos].from )
+ error("The positions are not in chromosomal order (%s:%d comes after %d)\n", line,stats->regions[tid].pos[npos].from,prev_pos);
+ stats->regions[tid].npos++;
+ }
+ if (line) free(line);
+ fclose(fp);
+ }
+
+ void destroy_regions(stats_t *stats)
+ {
+ int i;
+ for (i=0; i<stats->nregions; i++)
+ {
+ if ( !stats->regions[i].mpos ) continue;
+ free(stats->regions[i].pos);
+ }
+ if ( stats->regions ) free(stats->regions);
+ }
+
+ static int fetch_read(const bam1_t *bam_line, void *data)
+ {
+ collect_stats((bam1_t*)bam_line,(stats_t*)data);
+ return 1;
+ }
+
+
+ void error(const char *format, ...)
+ {
+ if ( !format )
+ {
+ printf("Version: %s\n", BAMCHECK_VERSION);
+ printf("About: The program collects statistics from BAM files. The output can be visualized using plot-bamcheck.\n");
+ printf("Usage: bamcheck [OPTIONS] file.bam\n");
+ printf(" bamcheck [OPTIONS] file.bam chr:from-to\n");
+ 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(" -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");
+ printf(" -m, --most-inserts <float> Report only the main part of inserts [0.99]\n");
+ printf(" -q, --trim-quality <int> The BWA trimming parameter [0]\n");
+ printf(" -r, --ref-seq <file> Reference sequence (required for GC-depth calculation).\n");
+ printf(" -t, --target-regions <file> Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n");
+ printf(" -s, --sam Input is SAM\n");
+ printf("\n");
+ }
+ else
+ {
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(stderr, format, ap);
+ va_end(ap);
+ }
+ exit(-1);
+ }
+
+ int main(int argc, char *argv[])
+ {
+ char *targets = NULL;
+ char *bam_fname = NULL;
+ samfile_t *sam = NULL;
+ char in_mode[5];
+
+ stats_t *stats = calloc(1,sizeof(stats_t));
+ stats->ngc = 200;
+ stats->nquals = 95;
+ stats->nbases = 300;
+ stats->nisize = 8000;
+ stats->max_len = 30;
+ stats->max_qual = 40;
+ stats->isize_main_bulk = 0.99; // There are always outliers at the far end
+ stats->gcd_bin_size = 20000;
+ stats->ngcd = 3e5; // 300k of 20k bins is enough to hold a genome 6Gbp big
+ stats->nref_seq = stats->gcd_bin_size;
+ stats->rseq_pos = -1;
+ stats->tid = stats->gcd_pos = -1;
+ stats->is_sorted = 1;
+ stats->cov_min = 1;
+ stats->cov_max = 1000;
+ stats->cov_step = 1;
+ stats->argc = argc;
+ stats->argv = argv;
+ stats->filter_readlen = -1;
+ stats->nindels = stats->nbases;
+
+ strcpy(in_mode, "rb");
+
+ static struct option loptions[] =
+ {
+ {"help",0,0,'h'},
+ {"remove-dups",0,0,'d'},
+ {"sam",0,0,'s'},
+ {"ref-seq",0,0,'r'},
+ {"coverage",0,0,'c'},
+ {"read-length",0,0,'l'},
+ {"insert-size",0,0,'i'},
+ {"most-inserts",0,0,'m'},
+ {"trim-quality",0,0,'q'},
+ {"target-regions",0,0,'t'},
+ {0,0,0,0}
+ };
+ int opt;
+ while ( (opt=getopt_long(argc,argv,"?hdsr:c:l:i:t:m:q:",loptions,NULL))>0 )
+ {
+ switch (opt)
+ {
+ case 'd': stats->rmdup=1; break;
+ case 's': strcpy(in_mode, "r"); break;
+ case 'r': stats->fai = fai_load(optarg);
+ if (stats->fai==0)
+ error("Could not load faidx: %s\n", optarg);
+ break;
+ case 'c': if ( sscanf(optarg,"%d,%d,%d",&stats->cov_min,&stats->cov_max,&stats->cov_step)!= 3 )
+ error("Unable to parse -c %s\n", optarg);
+ break;
+ case 'l': stats->filter_readlen = atoi(optarg); break;
+ case 'i': stats->nisize = atoi(optarg); break;
+ case 'm': stats->isize_main_bulk = atof(optarg); break;
+ case 'q': stats->trim_qual = atoi(optarg); break;
+ case 't': targets = optarg; break;
+ case '?':
+ case 'h': error(NULL);
+ default: error("Unknown argument: %s\n", optarg);
+ }
+ }
+ if ( optind<argc )
+ bam_fname = argv[optind++];
+
+ if ( !bam_fname )
+ {
+ if ( isatty(fileno((FILE *)stdin)) )
+ error(NULL);
+ bam_fname = "-";
+ }
+
+ // Init structures
+ // .. coverage bins and round buffer
+ if ( stats->cov_step > stats->cov_max - stats->cov_min + 1 )
+ {
+ stats->cov_step = stats->cov_max - stats->cov_min;
+ if ( stats->cov_step <= 0 )
+ stats->cov_step = 1;
+ }
+ stats->ncov = 3 + (stats->cov_max-stats->cov_min) / stats->cov_step;
+ stats->cov_max = stats->cov_min + ((stats->cov_max-stats->cov_min)/stats->cov_step +1)*stats->cov_step - 1;
+ stats->cov = calloc(sizeof(uint64_t),stats->ncov);
+ stats->cov_rbuf.size = stats->nbases*5;
+ stats->cov_rbuf.buffer = calloc(sizeof(int32_t),stats->cov_rbuf.size);
+ // .. bam
+ if ((sam = samopen(bam_fname, in_mode, NULL)) == 0)
+ error("Failed to open: %s\n", bam_fname);
+ 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,sizeof(uint64_t));
+ stats->del_cycles = calloc(stats->nbases,sizeof(uint64_t));
+ if ( targets )
+ init_regions(stats, targets);
+
+ // Collect statistics
+ if ( optind<argc )
+ {
+ // Collect stats in selected regions only
+ bam_index_t *bam_idx = bam_index_load(bam_fname);
+ if (bam_idx == 0)
+ error("Random alignment retrieval only works for indexed BAM files.\n");
+
+ int i;
+ for (i=optind; i<argc; i++)
+ {
+ int tid, beg, end;
+ bam_parse_region(stats->sam->header, argv[i], &tid, &beg, &end);
+ if ( tid < 0 ) continue;
+ bam_fetch(stats->sam->x.bam, bam_idx, tid, beg, end, stats, fetch_read);
+ }
+ bam_index_destroy(bam_idx);
+ }
+ else
+ {
+ // 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);
+
+ output_stats(stats);
+
+ bam_destroy1(bam_line);
+ samclose(stats->sam);
+ if (stats->fai) fai_destroy(stats->fai);
+ free(stats->cov_rbuf.buffer); free(stats->cov);
+ free(stats->quals_1st); free(stats->quals_2nd);
+ free(stats->gc_1st); free(stats->gc_2nd);
+ free(stats->isize_inward); free(stats->isize_outward); free(stats->isize_other);
+ free(stats->gcd);
+ free(stats->rseq_buf);
+ free(stats->mpc_buf);
+ free(stats->acgt_cycles);
+ free(stats->read_lengths);
+ free(stats->insertions);
+ free(stats->deletions);
+ free(stats->ins_cycles);
+ free(stats->del_cycles);
+ destroy_regions(stats);
+ free(stats);
+
+ return 0;
+ }
+
+
+
projects / samtools.git / commitdiff