From: Petr Danecek Date: Wed, 5 Sep 2012 15:36:24 +0000 (+0100) Subject: Fix in insertion cycle calculation of rev reads X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=bfcd9b39b85184a8815529b245280fd45f190253 Fix in insertion cycle calculation of rev reads --- diff --git a/misc/bamcheck.c b/misc/bamcheck.c index 8c54388..532d105 100644 --- a/misc/bamcheck.c +++ b/misc/bamcheck.c @@ -1,6 +1,6 @@ /* Author: petr.danecek@sanger - gcc -Wall -Winline -g -O2 -I ~/git/samtools bamcheck.c -o bamcheck -lm -lz -L ~/git/samtools -lbam + gcc -Wall -Winline -g -O2 -I ~/git/samtools bamcheck.c -o bamcheck -lm -lz -L ~/git/samtools -lbam -lpthread Assumptions, approximations and other issues: - GC-depth graph does not split reads, the starting position determines which bin is incremented. @@ -15,7 +15,7 @@ */ -#define BAMCHECK_VERSION "2012-04-24" +#define BAMCHECK_VERSION "2012-09-04" #define _ISOC99_SOURCE #include @@ -26,6 +26,7 @@ #include #include #include +#include #include "faidx.h" #include "khash.h" #include "sam.h" @@ -129,6 +130,7 @@ typedef struct 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 + uint32_t gcd_ref_size; // The approximate size of the genome int32_t tid, gcd_pos; // Position of the current bin int32_t pos; // Position of the last read @@ -139,11 +141,11 @@ typedef struct 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 + uint8_t *rseq_buf; // A buffer for reference sequence to check the mismatches against + int mrseq_buf; // The size of the buffer + int32_t rseq_pos; // The coordinate of the first base in the buffer + int32_t nrseq_buf; // The used part of the buffer + uint64_t *mpc_buf; // Mismatches per cycle // Filters int filter_readlen; @@ -291,9 +293,10 @@ void count_indels(stats_t *stats,bam1_t *bam_line) if ( cig==1 ) { - 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); + int idx = is_fwd ? icycle : read_len-icycle-ncig; + 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, %s:%d %s\n", idx,stats->nbases, stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,bam1_qname(bam_line)); if ( is_1st ) stats->ins_cycles_1st[idx]++; else @@ -316,7 +319,8 @@ void count_indels(stats_t *stats,bam1_t *bam_line) stats->deletions[ncig-1]++; continue; } - icycle += ncig; + if ( cig!=3 && cig!=5 ) + icycle += ncig; } } @@ -360,11 +364,14 @@ void count_mismatches_per_cycle(stats_t *stats,bam1_t *bam_line) icycle += ncig; continue; } + // Ignore H and N CIGARs. The letter are inserted e.g. by TopHat and often require very large + // chunk of refseq in memory. Not very frequent and not noticable in the stats. + if ( cig==3 || cig==5 ) continue; if ( cig!=0 ) - error("TODO: cigar %d, %s\n", cig,bam1_qname(bam_line)); + error("TODO: cigar %d, %s:%d %s\n", cig,stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,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); + if ( ncig+iref > stats->nrseq_buf ) + error("FIXME: %d+%d > %d, %s, %s:%d\n",ncig,iref,stats->nrseq_buf, bam1_qname(bam_line),stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1); int im; for (im=0; im= 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; + int size = stats->mrseq_buf; // 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; @@ -458,24 +465,25 @@ void read_ref_seq(stats_t *stats,int32_t tid,int32_t pos) ptr++; nread++; } - if ( nread < stats->nref_seq ) + if ( nread < stats->mrseq_buf ) { - memset(ptr,0, stats->nref_seq - nread); - nread = stats->nref_seq; + memset(ptr,0, stats->mrseq_buf - nread); + nread = stats->mrseq_buf; } - stats->rseq_len = nread; - stats->rseq_pos = pos; - stats->tid = tid; + stats->nrseq_buf = nread; + stats->rseq_pos = pos; + stats->tid = tid; } -float fai_gc_content(stats_t *stats) +float fai_gc_content(stats_t *stats, int pos, int len) { uint32_t gc,count,c; - int i,size = stats->rseq_len; + int i = pos - stats->rseq_pos, ito = i + len; + assert( i>=0 && ito<=stats->nrseq_buf ); // Count GC content gc = count = 0; - for (i=0; irseq_buf[i]; if ( c==2 || c==4 ) @@ -489,6 +497,37 @@ float fai_gc_content(stats_t *stats) return count ? (float)gc/count : 0; } +void realloc_rseq_buffer(stats_t *stats) +{ + int n = stats->nbases*10; + if ( stats->gcd_bin_size > n ) n = stats->gcd_bin_size; + if ( stats->mrseq_bufrseq_buf = realloc(stats->rseq_buf,sizeof(uint8_t)*n); + stats->mrseq_buf = n; + } +} + +void realloc_gcd_buffer(stats_t *stats, int seq_len) +{ + if ( seq_len >= stats->gcd_bin_size ) + error("The --GC-depth bin size (%d) is set too low for the read length %d\n", stats->gcd_bin_size, seq_len); + + int n = 1 + stats->gcd_ref_size / (stats->gcd_bin_size - seq_len); + if ( n <= stats->igcd ) + error("Uh: n=%d igcd=%d\n", n,stats->igcd ); + + if ( n >= 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->ngcd = n; + } + + realloc_rseq_buffer(stats); +} void realloc_buffers(stats_t *stats, int seq_len) { @@ -535,22 +574,22 @@ void realloc_buffers(stats_t *stats, int seq_len) 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_1st + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t)); + memset(stats->ins_cycles_1st + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); 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->ins_cycles_2nd + stats->nbases + 1, 0, (n+1-stats->nbases)*sizeof(uint64_t)); + memset(stats->ins_cycles_2nd + stats->nbases + 1, 0, (n-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)); + memset(stats->del_cycles_1st + stats->nbases + 1, 0, (n-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)); + memset(stats->del_cycles_2nd + stats->nbases + 1, 0, (n-stats->nbases)*sizeof(uint64_t)); stats->nbases = n; @@ -564,6 +603,8 @@ void realloc_buffers(stats_t *stats, int seq_len) free(stats->cov_rbuf.buffer); stats->cov_rbuf.buffer = rbuffer; stats->cov_rbuf.size = seq_len*5; + + realloc_rseq_buffer(stats); } void collect_stats(bam1_t *bam_line, stats_t *stats) @@ -757,44 +798,45 @@ void collect_stats(bam1_t *bam_line, stats_t *stats) if ( stats->tid==-1 || stats->tid!=bam_line->core.tid ) round_buffer_flush(stats,-1); - // Mismatches per cycle and GC-depth graph + // Mismatches per cycle and GC-depth graph. For simplicity, reads overlapping GCD bins + // are not splitted which results in up to seq_len-1 overlaps. The default bin size is + // 20kbp, so the effect is negligible. 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 ) + int inc_ref = 0, inc_gcd = 0; + // First pass or new chromosome + if ( stats->rseq_pos==-1 || stats->tid != bam_line->core.tid ) { inc_ref=1; inc_gcd=1; } + // Read goes beyond the end of the rseq buffer + else if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+readlen ) { inc_ref=1; inc_gcd=1; } + // Read overlaps the next gcd bin + else if ( stats->gcd_pos+stats->gcd_bin_size < bam_line->core.pos+readlen ) + { + inc_gcd = 1; + if ( stats->rseq_pos+stats->nrseq_buf < bam_line->core.pos+stats->gcd_bin_size ) inc_ref = 1; + } + if ( inc_gcd ) { - 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); + realloc_gcd_buffer(stats, readlen); + if ( inc_ref ) + read_ref_seq(stats,bam_line->core.tid,bam_line->core.pos); + stats->gcd_pos = bam_line->core.pos; + stats->gcd[ stats->igcd ].gc = fai_gc_content(stats, stats->gcd_pos, stats->gcd_bin_size); } + count_mismatches_per_cycle(stats,bam_line); } + // No reference and first pass, new chromosome or sequence going beyond the end of the gcd bin 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)); - } + realloc_gcd_buffer(stats, readlen); } - 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 ) @@ -1001,6 +1043,8 @@ 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 (fwd), .. (rev) , number of deletions (fwd), .. (rev)\n"); for (ilen=0; ilen<=stats->nbases; ilen++) { + // For deletions we print the index of the cycle before the deleted base (1-based) and for insertions + // the index of the cycle of the first inserted base (also 1-based) 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]); } @@ -1235,6 +1279,7 @@ void error(const char *format, ...) printf(" -d, --remove-dups Exlude from statistics reads marked as duplicates\n"); printf(" -f, --required-flag Required flag, 0 for unset [0]\n"); printf(" -F, --filtering-flag Filtering flag, 0 for unset [0]\n"); + printf(" --GC-depth Bin size for GC-depth graph and the maximum reference length [2e4,6e9]\n"); printf(" -h, --help This help message\n"); printf(" -i, --insert-size Maximum insert size [8000]\n"); printf(" -I, --id Include only listed read group or sample name\n"); @@ -1272,11 +1317,10 @@ int main(int argc, char *argv[]) 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->gcd_bin_size = 20e3; + stats->gcd_ref_size = 3e9; stats->rseq_pos = -1; - stats->tid = stats->gcd_pos = -1; + stats->tid = stats->gcd_pos = stats->igcd = -1; stats->is_sorted = 1; stats->cov_min = 1; stats->cov_max = 1000; @@ -1293,20 +1337,21 @@ int main(int argc, char *argv[]) {"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'}, + {"ref-seq",1,0,'r'}, + {"coverage",1,0,'c'}, + {"read-length",1,0,'l'}, + {"insert-size",1,0,'i'}, + {"most-inserts",1,0,'m'}, + {"trim-quality",1,0,'q'}, {"target-regions",0,0,'t'}, - {"required-flag",0,0,'f'}, + {"required-flag",1,0,'f'}, {"filtering-flag",0,0,'F'}, - {"id",0,0,'I'}, + {"id",1,0,'I'}, + {"GC-depth",1,0,1}, {0,0,0,0} }; int opt; - while ( (opt=getopt_long(argc,argv,"?hdsr:c:l:i:t:m:q:f:F:I:",loptions,NULL))>0 ) + while ( (opt=getopt_long(argc,argv,"?hdsr:c:l:i:t:m:q:f:F:I:1:",loptions,NULL))>0 ) { switch (opt) { @@ -1318,6 +1363,14 @@ int main(int argc, char *argv[]) if (stats->fai==0) error("Could not load faidx: %s\n", optarg); break; + case 1 : { + float flen,fbin; + if ( sscanf(optarg,"%f,%f",&fbin,&flen)!= 2 ) + error("Unable to parse --GC-depth %s\n", optarg); + stats->gcd_bin_size = fbin; + stats->gcd_ref_size = flen; + } + 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; @@ -1370,7 +1423,6 @@ int main(int argc, char *argv[]) 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)); @@ -1380,6 +1432,7 @@ int main(int argc, char *argv[]) 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)); + realloc_rseq_buffer(stats); if ( targets ) init_regions(stats, targets); @@ -1434,7 +1487,7 @@ int main(int argc, char *argv[]) free(stats); if ( stats->rg_hash ) kh_destroy(kh_rg, stats->rg_hash); - return 0; + return 0; }