New upstream version 1.7 (c5c1bb21) · Commits · Debian Med / bcftools

Makefile

+5 −5

Original line number	Diff line number	Diff line
		@@ -93,7 +93,7 @@ endif

		include config.mk

		PACKAGE_VERSION = 1.6
		PACKAGE_VERSION = 1.7

		# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
		# description of the working tree: either a release tag with the same value
		@@ -148,7 +148,7 @@ PLATFORM := $(shell uname -s)
		endif
		ifeq "$(PLATFORM)" "Darwin"
		$(PLUGINS): \| bcftools
		PLUGIN_FLAGS = -bundle -bundle_loader bcftools
		PLUGIN_FLAGS = -bundle -bundle_loader bcftools -Wl,-undefined,dynamic_lookup
		else
		PLUGIN_FLAGS = -fPIC -shared
		endif
		@@ -272,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
		# bcftools.1 is a generated file from the asciidoc bcftools.txt file.
		# Since there is no make dependency, bcftools.1 can be out-of-date and
		# make docs can be run to update if asciidoc is available
		install: $(PROG) $(PLUGINS)
		install: $(PROGRAMS) $(PLUGINS)
		$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
		$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
		$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
		@@ -280,7 +280,7 @@ install: $(PROG) $(PLUGINS)
		$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)

		clean: testclean clean-plugins
		-rm -f gmon.out .o ~ $(PROG) version.h plugins/.so plugins/.P
		-rm -f gmon.out .o ~ $(PROGRAMS) version.h plugins/.so plugins/.P
		-rm -rf .dSYM plugins/.dSYM test/*.dSYM

		clean-plugins:
		@@ -288,7 +288,7 @@ clean-plugins:
		-rm -rf plugins/*.dSYM

		testclean:
		-rm -f test/.o test/~ $(TEST_PROG)
		-rm -f test/.o test/~ $(TEST_PROGRAMS)

		distclean: clean
		-rm -f config.cache config.h config.log config.mk config.status

NEWS

+37 −0

Original line number	Diff line number	Diff line
		## Release 1.7 (February 2018)

		* `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields
		and missing values. New GT=ref,alt,mis etc keywords, check the documenation
		for details.

		* `query`: Only matching expression are printed when both the -f and -i/-e
		expressions contain genotype fields. Note that this changes the original
		behavior. Previously all samples were output when one matching sample was
		found. This functionality can be achieved by pre-filtering with view and then
		streaming to query. Compare
		bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
		and
		bcftools view -i'GT="alt"' file.bcf -Ou \| bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

		* `annotate`: New -k, --keep-sites option

		* `consensus`: Fix --iupac-codes output

		* `csq`: Homs always considered phased and other fixes

		* `norm`: Make `-c none` work and remove `query -c`

		* `roh`: Fix errors in the RG output

		* `stats`: Allow IUPAC ambiguity codes in the reference file; report the number of missing genotypes

		* `+fill-tags`: Add ExcHet annotation

		* `+setGt`: Fix bug in binom.test calculation, previously it worked only for nAlt<nRef!

		* `+split`: New plugin to split a multi-sample file into single-sample files in one go

		* Improve python3 compatibility in plotting scripts



		## Release 1.6 (September 2017)

		* New `sort` command.

bcftools.h

+17 −0

Original line number	Diff line number	Diff line
		@@ -63,6 +63,23 @@ static inline char gt2iupac(char a, char b)
		return iupac[(int)a][(int)b];
		}

		static inline int iupac_consistent(char iupac, char nt)
		{
		static const char iupac_mask[90] = {
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
		0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,14,2,
		13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10
		};
		if ( iupac > 89 ) return 0;
		if ( nt > 90 ) nt -= 32; // lowercase
		if ( nt=='A' ) nt = 1;
		else if ( nt=='C' ) nt = 2;
		else if ( nt=='G' ) nt = 4;
		else if ( nt=='T' ) nt = 8;
		return iupac_mask[(int)iupac] & nt ? 1 : 0;
		}

		static inline char nt_to_upper(char nt)
		{
		if ( nt < 97 ) return nt;

consensus.c

+9 −4

Original line number	Diff line number	Diff line
		@@ -77,6 +77,7 @@ typedef struct
		rbuf_t vcf_rbuf;
		bcf1_t **vcf_buf;
		int nvcf_buf, rid;
		char *chr;

		regidx_t *mask;
		regitr_t *itr;
		@@ -121,6 +122,8 @@ static void destroy_chain(args_t *args)
		free(chain->block_lengths);
		free(chain);
		chain = NULL;
		free(args->chr);
		args->chr = NULL;
		}

		static void print_chain(args_t *args)
		@@ -162,7 +165,7 @@ static void print_chain(args_t *args)
		score += chain->block_lengths[n];
		}
		score += last_block_size;
		fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, bcf_hdr_id2name(args->hdr,args->rid), ref_end_pos, chain->ori_pos, ref_end_pos, bcf_hdr_id2name(args->hdr,args->rid), alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);
		fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);
		for (n=0; n<chain->num; n++) {
		fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]);
		}
		@@ -248,6 +251,7 @@ static void destroy_data(args_t *args)
		if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]);
		free(args->vcf_buf);
		free(args->fa_buf.s);
		free(args->chr);
		if ( args->mask ) regidx_destroy(args->mask);
		if ( args->itr ) regitr_destroy(args->itr);
		if ( args->chain_fname )
		@@ -276,6 +280,7 @@ static void init_region(args_t args, char line)
		else to--;
		}
		}
		args->chr = strdup(line);
		args->rid = bcf_hdr_name2id(args->hdr,line);
		if ( args->rid<0 ) fprintf(stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname);
		args->fa_buf.l = 0;
		@@ -380,7 +385,7 @@ static void apply_variant(args_t args, bcf1_t rec)
		if ( regidx_overlap(args->mask, chr,start,end,NULL) ) return;
		}

		int i, ialt = 1;
		int i, ialt = 1; // the alternate allele
		if ( args->isample >= 0 )
		{
		bcf_unpack(rec, BCF_UN_FMT);
		@@ -417,6 +422,7 @@ static void apply_variant(args_t args, bcf1_t rec)
		{
		char ial = rec->d.allele[ialt][0];
		char jal = rec->d.allele[jalt][0];
		if ( !ialt ) ialt = jalt; // only ialt is used, make sure 0/1 is not ignored
		rec->d.allele[ialt][0] = gt2iupac(ial,jal);
		}
		}
		@@ -565,11 +571,10 @@ static void apply_variant(args_t args, bcf1_t rec)

		static void mask_region(args_t args, char seq, int len)
		{
		char chr = (char)bcf_hdr_id2name(args->hdr,args->rid);
		int start = args->fa_src_pos - len;
		int end = args->fa_src_pos;

		if ( !regidx_overlap(args->mask, chr,start,end, args->itr) ) return;
		if ( !regidx_overlap(args->mask, args->chr,start,end, args->itr) ) return;

		int idx_start, idx_end, i;
		while ( regitr_overlap(args->itr) )

convert.c

+29 −1

Original line number	Diff line number	Diff line
		/* convert.c -- functions for converting between VCF/BCF and related formats.

		Copyright (C) 2013-2017 Genome Research Ltd.
		Copyright (C) 2013-2018 Genome Research Ltd.

		Author: Petr Danecek <pd3@sanger.ac.uk>

		@@ -92,6 +92,7 @@ struct _convert_t
		int ndat;
		char *undef_info_tag;
		int allow_undef_tags;
		uint8_t **subset_samples;
		};

		typedef struct
		@@ -174,6 +175,24 @@ static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx)
		}
		return ((int32_t*)bcf_array)[idx];
		}
		static inline void _copy_field(char src, uint32_t len, int idx, kstring_t str)
		{
		int n = 0, ibeg = 0;
		while ( src[ibeg] && ibeg<len && n < idx )
		{
		if ( src[ibeg]==',' ) n++;
		ibeg++;
		}
		if ( ibeg==len ) { kputc('.', str); return; }

		int iend = ibeg;
		while ( src[iend] && src[iend]!=',' && iend<len ) iend++;

		if ( iend>ibeg )
		kputsn(src+ibeg, iend-ibeg, str);
		else
		kputc('.', str);
		}
		static void process_info(convert_t convert, bcf1_t line, fmt_t fmt, int isample, kstring_t str)
		{
		if ( fmt->id<0 )
		@@ -232,6 +251,7 @@ static void process_info(convert_t convert, bcf1_t line, fmt_t *fmt, int isamp
		case BCF_BT_INT16: BRANCH(int16_t, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break;
		case BCF_BT_INT32: BRANCH(int32_t, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break;
		case BCF_BT_FLOAT: BRANCH(float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break;
		case BCF_BT_CHAR: _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break;
		default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;
		}
		#undef BRANCH
		@@ -288,6 +308,8 @@ static void process_format(convert_t convert, bcf1_t line, fmt_t *fmt, int isa
		else
		kputw(ival, str);
		}
		else if ( fmt->fmt->type == BCF_BT_CHAR )
		_copy_field((char)(fmt->fmt->p + isamplefmt->fmt->size), fmt->fmt->size, fmt->subscript, str);
		else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
		}
		else
		@@ -1312,6 +1334,9 @@ int convert_line(convert_t convert, bcf1_t line, kstring_t *str)
		}
		for (js=0; js<convert->nsamples; js++)
		{
		// Skip samples when filtering was requested
		if ( convert->subset_samples && !(convert->subset_samples)[js] ) continue;

		// Here comes a hack designed for TBCSQ. When running on large files,
		// such as 1000GP, there are too many empty fields in the output and
		// it's very very slow. Therefore in case the handler does not add
		@@ -1362,6 +1387,9 @@ int convert_set_option(convert_t *convert, enum convert_option opt, ...)
		case allow_undef_tags:
		convert->allow_undef_tags = va_arg(args, int);
		break;
		case subset_samples:
		convert->subset_samples = va_arg(args, uint8_t**);
		break;
		default:
		ret = -1;
		}