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Release 1.6: sort command; filtering and other improvements
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| /* The MIT License | ||
| Copyright (c) 2014 Genome Research Ltd. | ||
| Copyright (c) 2014-2017 Genome Research Ltd. | ||
| Author: Petr Danecek <[email protected]> | ||
|
|
@@ -39,6 +39,16 @@ | |
| #include "regidx.h" | ||
| #include "bcftools.h" | ||
| #include "rbuf.h" | ||
| #include "filter.h" | ||
|
|
||
| // Logic of the filters: include or exclude sites which match the filters? | ||
| #define FLT_INCLUDE 1 | ||
| #define FLT_EXCLUDE 2 | ||
|
|
||
| #define PICK_REF 1 | ||
| #define PICK_ALT 2 | ||
| #define PICK_LONG 4 | ||
| #define PICK_SHORT 8 | ||
|
|
||
| typedef struct | ||
| { | ||
|
|
@@ -75,12 +85,16 @@ typedef struct | |
| chain_t *chain; // chain structure to store the sequence of ungapped blocks between the ref and alt sequences | ||
| // Note that the chain is re-initialised for each chromosome/seq_region | ||
|
|
||
| filter_t *filter; | ||
| char *filter_str; | ||
| int filter_logic; // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE | ||
|
|
||
| bcf_srs_t *files; | ||
| bcf_hdr_t *hdr; | ||
| FILE *fp_out; | ||
| FILE *fp_chain; | ||
| char **argv; | ||
| int argc, output_iupac, haplotype, isample; | ||
| int argc, output_iupac, haplotype, allele, isample; | ||
| char *fname, *ref_fname, *sample, *output_fname, *mask_fname, *chain_fname; | ||
| } | ||
| args_t; | ||
|
|
@@ -195,7 +209,7 @@ static void init_data(args_t *args) | |
| args->isample = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->sample); | ||
| if ( args->isample<0 ) error("No such sample: %s\n", args->sample); | ||
| } | ||
| if ( args->haplotype && args->isample<0 ) | ||
| if ( (args->haplotype || args->allele) && args->isample<0 ) | ||
| { | ||
| if ( bcf_hdr_nsamples(args->hdr) > 1 ) error("The --sample option is expected with --haplotype\n"); | ||
| args->isample = 0; | ||
|
|
@@ -220,10 +234,14 @@ static void init_data(args_t *args) | |
| if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno)); | ||
| } | ||
| else args->fp_out = stdout; | ||
| if ( args->isample<0 ) fprintf(stderr,"Note: the --sample option not given, applying all records\n"); | ||
| if ( args->filter_str ) | ||
| args->filter = filter_init(args->hdr, args->filter_str); | ||
| } | ||
|
|
||
| static void destroy_data(args_t *args) | ||
| { | ||
| if (args->filter) filter_destroy(args->filter); | ||
| bcf_sr_destroy(args->files); | ||
| int i; | ||
| for (i=0; i<args->vcf_rbuf.m; i++) | ||
|
|
@@ -287,9 +305,16 @@ static bcf1_t **next_vcf_line(args_t *args) | |
| int i = rbuf_shift(&args->vcf_rbuf); | ||
| return &args->vcf_buf[i]; | ||
| } | ||
| else if ( bcf_sr_next_line(args->files) ) | ||
| while ( bcf_sr_next_line(args->files) ) | ||
| { | ||
| if ( args->filter ) | ||
| { | ||
| int is_ok = filter_test(args->filter, bcf_sr_get_line(args->files,0), NULL); | ||
| if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1; | ||
| if ( !is_ok ) continue; | ||
| } | ||
| return &args->files->readers[0].buffer[0]; | ||
|
|
||
| } | ||
| return NULL; | ||
| } | ||
| static void unread_vcf_line(args_t *args, bcf1_t **rec_ptr) | ||
|
|
@@ -358,33 +383,36 @@ static void apply_variant(args_t *args, bcf1_t *rec) | |
| int i, ialt = 1; | ||
| if ( args->isample >= 0 ) | ||
| { | ||
| bcf_unpack(rec, BCF_UN_FMT); | ||
| bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT"); | ||
| if ( !fmt ) return; | ||
|
|
||
| if ( fmt->type!=BCF_BT_INT8 ) | ||
| error("Todo: GT field represented with BCF_BT_INT8, too many alleles at %s:%d?\n",bcf_seqname(args->hdr,rec),rec->pos+1); | ||
| uint8_t *ptr = fmt->p + fmt->size*args->isample; | ||
|
|
||
| if ( args->haplotype ) | ||
| { | ||
| if ( args->haplotype > fmt->n ) error("Can't apply %d-th haplotype at %s:%d\n", args->haplotype,bcf_seqname(args->hdr,rec),rec->pos+1); | ||
| uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample + args->haplotype - 1; | ||
| ialt = bcf_dec_int1(ptr, fmt->type, &ignore); | ||
| ialt = ptr[args->haplotype-1]; | ||
| if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return; | ||
| ialt = bcf_gt_allele(ialt); | ||
| } | ||
| else if ( args->output_iupac ) | ||
| { | ||
| uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample; | ||
| ialt = bcf_dec_int1(ptr, fmt->type, &ignore); | ||
| ialt = ptr[0]; | ||
| if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return; | ||
| ialt = bcf_gt_allele(ialt); | ||
|
|
||
| int jalt; | ||
| if ( fmt->n>1 ) | ||
| { | ||
| ptr = fmt->p + fmt->size*args->isample + 1; | ||
| jalt = bcf_dec_int1(ptr, fmt->type, &ignore); | ||
| jalt = ptr[1]; | ||
| if ( bcf_gt_is_missing(jalt) || jalt==bcf_int32_vector_end ) jalt = ialt; | ||
| else jalt = bcf_gt_allele(jalt); | ||
| } | ||
| else jalt = ialt; | ||
| if ( rec->n_allele <= ialt || rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1); | ||
| if ( rec->n_allele <= ialt || rec->n_allele <= jalt ) error("Invalid VCF, too few ALT alleles at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1); | ||
| if ( ialt!=jalt && !rec->d.allele[ialt][1] && !rec->d.allele[jalt][1] ) // is this a het snp? | ||
| { | ||
| char ial = rec->d.allele[ialt][0]; | ||
|
|
@@ -394,13 +422,40 @@ static void apply_variant(args_t *args, bcf1_t *rec) | |
| } | ||
| else | ||
| { | ||
| int is_hom = 1; | ||
| for (i=0; i<fmt->n; i++) | ||
| { | ||
| uint8_t *ignore, *ptr = fmt->p + fmt->size*args->isample + i; | ||
| ialt = bcf_dec_int1(ptr, fmt->type, &ignore); | ||
| if ( bcf_gt_is_missing(ialt) || ialt==bcf_int32_vector_end ) return; | ||
| ialt = bcf_gt_allele(ialt); | ||
| if ( ialt ) break; | ||
| if ( bcf_gt_is_missing(ptr[i]) ) return; // ignore missing or half-missing genotypes | ||
| if ( ptr[i]==bcf_int32_vector_end ) break; | ||
| ialt = bcf_gt_allele(ptr[i]); | ||
| if ( i>0 && ialt!=bcf_gt_allele(ptr[i-1]) ) { is_hom = 0; break; } | ||
| } | ||
| if ( !is_hom ) | ||
| { | ||
| int prev_len = 0, jalt; | ||
| for (i=0; i<fmt->n; i++) | ||
| { | ||
| if ( ptr[i]==bcf_int32_vector_end ) break; | ||
| jalt = bcf_gt_allele(ptr[i]); | ||
| if ( rec->n_allele <= jalt ) error("Broken VCF, too few alts at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1); | ||
| if ( args->allele & (PICK_LONG|PICK_SHORT) ) | ||
| { | ||
| int len = jalt==0 ? rec->rlen : strlen(rec->d.allele[jalt]); | ||
| if ( i==0 ) ialt = jalt, prev_len = len; | ||
| else if ( len == prev_len ) | ||
| { | ||
| if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt, prev_len = len; | ||
| else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt, prev_len = len; | ||
| } | ||
| else if ( args->allele & PICK_LONG && len > prev_len ) ialt = jalt, prev_len = len; | ||
| else if ( args->allele & PICK_SHORT && len < prev_len ) ialt = jalt, prev_len = len; | ||
| } | ||
| else | ||
| { | ||
| if ( args->allele & PICK_REF && jalt==0 ) ialt = jalt; | ||
| else if ( args->allele & PICK_ALT && ialt==0 ) ialt = jalt; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| if ( !ialt ) return; // ref allele | ||
|
|
@@ -623,12 +678,21 @@ static void usage(args_t *args) | |
| fprintf(stderr, " information, such as INFO/AD or FORMAT/AD.\n"); | ||
| fprintf(stderr, "Usage: bcftools consensus [OPTIONS] <file.vcf>\n"); | ||
| fprintf(stderr, "Options:\n"); | ||
| fprintf(stderr, " -c, --chain <file> write a chain file for liftover\n"); | ||
| fprintf(stderr, " -e, --exclude <expr> exclude sites for which the expression is true (see man page for details)\n"); | ||
| fprintf(stderr, " -f, --fasta-ref <file> reference sequence in fasta format\n"); | ||
| fprintf(stderr, " -H, --haplotype <1|2> apply variants for the given haplotype\n"); | ||
| fprintf(stderr, " -i, --iupac-codes output variants in the form of IUPAC ambiguity codes\n"); | ||
| fprintf(stderr, " -H, --haplotype <which> choose which allele to use from the FORMAT/GT field, note\n"); | ||
| fprintf(stderr, " the codes are case-insensitive:\n"); | ||
| fprintf(stderr, " 1: first allele from GT\n"); | ||
| fprintf(stderr, " 2: second allele\n"); | ||
| fprintf(stderr, " R: REF allele in het genotypes\n"); | ||
| fprintf(stderr, " A: ALT allele\n"); | ||
| fprintf(stderr, " LR,LA: longer allele and REF/ALT if equal length\n"); | ||
| fprintf(stderr, " SR,SA: shorter allele and REF/ALT if equal length\n"); | ||
| fprintf(stderr, " -i, --include <expr> select sites for which the expression is true (see man page for details)\n"); | ||
| fprintf(stderr, " -I, --iupac-codes output variants in the form of IUPAC ambiguity codes\n"); | ||
| fprintf(stderr, " -m, --mask <file> replace regions with N\n"); | ||
| fprintf(stderr, " -o, --output <file> write output to a file [standard output]\n"); | ||
| fprintf(stderr, " -c, --chain <file> write a chain file for liftover\n"); | ||
| fprintf(stderr, " -s, --sample <name> apply variants of the given sample\n"); | ||
| fprintf(stderr, "Examples:\n"); | ||
| fprintf(stderr, " # Get the consensus for one region. The fasta header lines are then expected\n"); | ||
|
|
@@ -645,8 +709,10 @@ int main_consensus(int argc, char *argv[]) | |
|
|
||
| static struct option loptions[] = | ||
| { | ||
| {"exclude",required_argument,NULL,'e'}, | ||
| {"include",required_argument,NULL,'i'}, | ||
| {"sample",1,0,'s'}, | ||
| {"iupac-codes",0,0,'i'}, | ||
| {"iupac-codes",0,0,'I'}, | ||
| {"haplotype",1,0,'H'}, | ||
| {"output",1,0,'o'}, | ||
| {"fasta-ref",1,0,'f'}, | ||
|
|
@@ -655,19 +721,32 @@ int main_consensus(int argc, char *argv[]) | |
| {0,0,0,0} | ||
| }; | ||
| int c; | ||
| while ((c = getopt_long(argc, argv, "h?s:1iH:f:o:m:c:",loptions,NULL)) >= 0) | ||
| while ((c = getopt_long(argc, argv, "h?s:1Ii:e:H:f:o:m:c:",loptions,NULL)) >= 0) | ||
| { | ||
| switch (c) | ||
| { | ||
| case 's': args->sample = optarg; break; | ||
| case 'o': args->output_fname = optarg; break; | ||
| case 'i': args->output_iupac = 1; break; | ||
| case 'I': args->output_iupac = 1; break; | ||
| case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break; | ||
| case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break; | ||
| case 'f': args->ref_fname = optarg; break; | ||
| case 'm': args->mask_fname = optarg; break; | ||
| case 'c': args->chain_fname = optarg; break; | ||
| case 'H': | ||
| args->haplotype = optarg[0] - '0'; | ||
| if ( args->haplotype <=0 ) error("Expected positive integer with --haplotype\n"); | ||
| if ( !strcasecmp(optarg,"R") ) args->allele |= PICK_REF; | ||
| else if ( !strcasecmp(optarg,"A") ) args->allele |= PICK_ALT; | ||
| else if ( !strcasecmp(optarg,"L") ) args->allele |= PICK_LONG|PICK_REF; | ||
| else if ( !strcasecmp(optarg,"S") ) args->allele |= PICK_SHORT|PICK_REF; | ||
| else if ( !strcasecmp(optarg,"LR") ) args->allele |= PICK_LONG|PICK_REF; | ||
| else if ( !strcasecmp(optarg,"LA") ) args->allele |= PICK_LONG|PICK_ALT; | ||
| else if ( !strcasecmp(optarg,"SR") ) args->allele |= PICK_SHORT|PICK_REF; | ||
| else if ( !strcasecmp(optarg,"SA") ) args->allele |= PICK_SHORT|PICK_ALT; | ||
| else | ||
| { | ||
| args->haplotype = optarg[0] - '0'; | ||
| if ( args->haplotype <=0 ) error("Expected positive integer with --haplotype\n"); | ||
| } | ||
| break; | ||
| default: usage(args); break; | ||
| } | ||
|
|
||
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