Release 1.17

Author: daviesrob

.cirrus.yml

@@ -139,8 +139,8 @@ rockylinux_task:
 
 macosx_task:
   name: macosx + clang
-  osx_instance:
-    image: catalina-base
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-ventura-base:latest
 
   environment:
     CC: clang

LICENSE

@@ -9,7 +9,7 @@ the INSTALL document), the use of this software is governed by the GPL license.
 
 The MIT/Expat License
 
-Copyright (C) 2012-2021 Genome Research Ltd.
+Copyright (C) 2012-2023 Genome Research Ltd.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -40,7 +40,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
            vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \
            regidx.o smpl_ilist.o csq.o vcfbuf.o \
-           mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
+           mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \
            vcfsort.o cols.o extsort.o dist.o abuf.o \
            ccall.o em.o prob1.o kmin.o str_finder.o
 PLUGIN_OBJS = vcfplugin.o
@@ -104,7 +104,7 @@ endif
 
 include config.mk
 
-PACKAGE_VERSION = 1.16
+PACKAGE_VERSION = 1.17
 
 # 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
@@ -279,6 +279,8 @@ consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf
 mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
 bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h
 bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h
+bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h cigar_state.h
+read_consensus.o: read_consensus.c read_consensus.h cigar_state.h $(htslib_hts_h) $(htslib_sam_h)
 bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h)
 version.o: version.h version.c
 hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h

NEWS

@@ -1,6 +1,170 @@
-## Release 1.16 (18th August 2022)
+## Release 1.17 (21st February 2023)
+
+
+Changes affecting the whole of bcftools, or multiple commands:
+
+* The -i/-e filtering expressions
+
+    - Error checks were added to prevent incorrect use of vector arithmetics. For example,
+      when evaluating the sum of two vectors A and B, the resulting vector could contain
+      nonsense values when the input vectors were not of the same length. The fix introduces
+      the following logic:
+        - evaluate to C_i = A_i + B_i when length(A)==B(A) and set length(C)=length(A)
+        - evaluate to C_i = A_i + B_0 when length(B)=1 and set length(C)=length(A)
+        - evaluate to C_i = A_0 + B_i when length(A)=1 and set length(C)=length(B)
+        - throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1
+
+    - Arrays in Number=R tags can be now subscripted by alleles found in FORMAT/GT. For example,
+
+        FORMAT/AD[GT] > 10        .. require support of more than 10 reads for each allele
+        FORMAT/AD[0:GT] > 10      .. same as above, but in the first sample
+        sSUM(FORMAT/AD[GT]) > 20  .. require total sample depth bigger than 20
+
+* The commands `consensus -H` and `+split-vep -H`
+
+    - Drop unnecessary leading space in the first header column and newly print `#[1]columnName`
+      instead of the previous `# [1]columnName` (#1856)
+
+
+Changes affecting specific commands:
+
+* bcftools +allele-length
+
+    - Fix overflow for indels longer than 512bp and aggregate alleles equal or larger than
+      that in the same bin (#1837)
+
+* bcftools annotate
+
+    - Support sample reordering of annotation file (#1785)
+
+    - Restore lost functionality of the --pair-logic option (#1808)
+
+* bcftools call
+
+    - Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory
+      corruption (#1790)
+
+    - Fix a bug where indels constrained with `-C alleles -T` would sometimes be missed (#1706)
+
+* bcftools consensus
+
+    - BREAKING CHANGE: the option `-I, --iupac-codes` newly outputs IUPAC codes based on FORMAT/GT
+      of all samples. The `-s, --samples` and `-S, --samples-file` options can be used to subset
+      samples. In order to ignore samples and consider only the REF and ALT columns (the original
+      behavior prior to 1.17), run with `-s -` (#1828)
+
+* bcftools convert
+
+    - Make variantkey conversion work for sites without an ALT allele (#1806)
+
+* bcftool csq
+
+    - Fix a bug where a MNV with multiple consequences (e.g. missense + stop_gained)
+      would report only the less severe one (#1810)
+
+    - GFF file parsing was made slightly more flexible, newly ids can be just 'XXX'
+      rather than, for example, 'gene:XXX'
+
+    - New gff2gff perl script to fix GFF formatting differences
+
+* bcftools +fill-tags
+
+    - More of the available annotations are now added by the `-t all` option
+
+* bcftools +fixref
+
+    - New INFO/FIXREF annotation
+
+    - New -m swap mode
 
+* bcftools +mendelian
 
+    - The +mendelian plugin has been deprecated and replaced with +mendelian2. The
+      function of the plugin is the same but the command line options and the output
+      format has changed, and for this was introduced as a new plugin.
+
+* bcftools mpileup
+
+    - Most of the annotations generated by mpileup are now optional via the
+      `-a, --annotate` option and add several new (mostly experimental) annotations.
+
+    - New option `--indels-2.0` for an EXPERIMENTAL indel calling model. This model aims
+      to address some known deficiencies of the current indel calling algorithm, specifically,
+      it uses diploid reference consensus sequence. Note that in the current version it
+      has the potential to increase sensitivity but at the cost of decreased specificity.
+
+    - Make the FS annotation (Fisher exact test strand bias) functional and remove it
+      from the default annotations
+
+* bcftools norm
+
+    - New --multi-overlaps option allows to set overlapping alleles either to the
+      ref allele (the current default) or to a missing allele (#1764 and #1802)
+
+    - Fixed a bug in `-m -` which does not split missing FORMAT values correctly and
+      could lead to empty FORMAT fields such as `::` instead of the correct `:.:` (#1818)
+
+    - The `--atomize` option previously would not split complex indels such as C>GGG.
+      Newly these will be split into two records C>G and C>CGG (#1832)
+
+* bcftools query
+
+    - Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly
+      suppressed when the `-e` option contained a sample expression while the formatting
+      query did not. See #1783 for details.
+
+* bcftools +setGT
+
+    - Add new `--new-gt X` option (#1800)
+
+    - Add new `--target-gt r:FLOAT` option to randomly select a proportion of genotypes (#1850)
+
+    - Fix a bug where `-t ./x` mode was advertised as selecting both phased and unphased
+      half-missing genotypes, but was in fact selecting only unphased genotypes (#1844)
+
+* bcftools +split-vep
+
+    - New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize
+      consequences from a list of genes, or restrict output to the listed genes
+
+    - New `-H, --print-header` option to print the header with `-f`
+
+    - Work around a bug in the LOFTEE VEP plugin used to annotate gnomAD VCFs. There the
+      LoF_info subfield contains commas which, in general, makes it impossible to parse the
+      VEP subfields. The +split-vep plugin can now work with such files, replacing the offending
+      commas with slash (/) characters. See also https://github.com/Ensembl/ensembl-vep/issues/1351
+
+    - Newly the `-c, --columns` option can be omitted when a subfield is used in `-i/-e` filtering
+      expression. Note that `-c` may still have to be given when it is not possible to infer the
+      type of the subfield. Note that this is an experimental feature.
+
+* bcftools stats
+
+    - The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and
+      the `-s -` option were given but the expression did not include sample columns (1835)
+
+* bcftools +tag2tag
+
+    - Revamp of the plugin to allow wider range of tag conversions, specifically all combinations
+      from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT
+
+* bcftools +trio-dnm2
+
+    - New `-n, --strictly-novel` option to downplay alleles which violate Mendelian
+      inheritance but are not novel
+
+    - Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make
+      the indel settings more strict by default
+
+    - Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values
+
+* bcftools +variant-distance
+
+    - New option `-d, --direction` to choose the directionality: forward, reverse, nearest (the default)
+      or both (#1829)
+
+
+## Release 1.16 (18th August 2022)
 
 * New plugin `bcftools +variant-distance` to annotate records with distance to the
   nearest variant (#1690)
@@ -44,7 +208,6 @@ Changes affecting specific commands:
 
     - Custom genotypes (e.g. `-n c:1/1`) now correctly override ploidy
 
-
 ## Release 1.15.1 (7th April 2022)
 
 

abuf.c

@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2021-2022 Genome Research Ltd.
+   Copyright (c) 2021-2023 Genome Research Ltd.
 
    Author: Petr Danecek <[email protected]>
 
@@ -154,22 +154,33 @@ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial)
                 assert(atom);
                 if ( altb!='-' ) kputc(altb, &atom->alt);
                 if ( refb!='-' ) { kputc(refb, &atom->ref); atom->end++; }
+                continue;
             }
-            else
+            buf->natoms++;
+            hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
+            atom = &buf->atoms[buf->natoms-1];
+            atom->ref.l = 0;
+            atom->alt.l = 0;
+            kputc(refb, &atom->ref);
+            kputc(altb, &atom->alt);
+            atom->beg = atom->end = i;
+            atom->ial = ial;
+
+            if ( rlen!=alen && (i+1>=rlen || i+1>=alen) )   // the next base is an indel combined with SNV, e.g. C>GGG?
             {
                 buf->natoms++;
                 hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
                 atom = &buf->atoms[buf->natoms-1];
                 atom->ref.l = 0;
                 atom->alt.l = 0;
                 kputc(refb, &atom->ref);
-                kputc(altb, &atom->alt);
+                kputc(refb, &atom->alt);
                 atom->beg = atom->end = i;
                 atom->ial = ial;
             }
             continue;
         }
-        if ( i+1>=rlen || i+1>=alen )   // is the next base a deletion?
+        if ( i+1>=rlen || i+1>=alen )   // is the next base an indel?
         {
             buf->natoms++;
             hts_expand0(atom_t,buf->natoms,buf->matoms,buf->atoms);
@@ -742,6 +753,8 @@ void _abuf_split(abuf_t *buf, bcf1_t *rec)
             _split_table_overlap(buf, j, atom);
         }
     }
+    // _split_table_print(buf);
+    // _split_table_print_atoms(buf);
     assert( !buf->rbuf.n ); // all records should be flushed first in the SPLIT mode
 
     // Create the output records, transferring all annotations: