From 46fff753a4ba5c9d14719e0e485c5b3836c295db Mon Sep 17 00:00:00 2001 From: Daniel Cameron Date: Fri, 27 Jan 2023 14:18:47 +1100 Subject: [PATCH] Promoted VCF 4.4 out of draft status --- Makefile | 6 +++--- README.md | 5 ++--- VCFv4.4.draft.pdf => VCFv4.4.pdf | Bin VCFv4.4.draft.tex => VCFv4.4.tex | 9 ++------- index.md | 2 +- 5 files changed, 8 insertions(+), 14 deletions(-) rename VCFv4.4.draft.pdf => VCFv4.4.pdf (100%) rename VCFv4.4.draft.tex => VCFv4.4.tex (99%) diff --git a/Makefile b/Makefile index 7d8376e23..a8a28824e 100644 --- a/Makefile +++ b/Makefile @@ -13,7 +13,7 @@ PDFS = BCFv1_qref.pdf \ VCFv4.1.pdf \ VCFv4.2.pdf \ VCFv4.3.pdf \ - VCFv4.4.draft.pdf + VCFv4.4.pdf pdf: $(PDFS:%=new/%) @@ -29,7 +29,7 @@ new/SAMtags.pdf diff/SAMtags.pdf: SAMtags.tex new/SAMtags.ver new/VCFv4.1.pdf diff/VCFv4.1.pdf: VCFv4.1.tex new/VCFv4.1.ver new/VCFv4.2.pdf diff/VCFv4.2.pdf: VCFv4.2.tex new/VCFv4.2.ver new/VCFv4.3.pdf diff/VCFv4.3.pdf: VCFv4.3.tex new/VCFv4.3.ver -new/VCFv4.4.draft.pdf diff/VCFv4.4.draft.pdf: VCFv4.4.draft.tex new/VCFv4.4.draft.ver +new/VCFv4.4.pdf diff/VCFv4.4.pdf: VCFv4.4.tex new/VCFv4.4.ver # Set LATEXMK to "scripts/rerun.sh new/$* $(PDFLATEX)" to use the previous # controller script, e.g., if your installation does not have latexmk. @@ -48,7 +48,7 @@ new/BEDv1.pdf: LATEXMK_ENGINE = --lualatex new/CRAMv2.1.ver new/CRAMv3.ver: img/CRAMFileFormat2-1-fig001.png img/CRAMFileFormat2-1-fig002.png img/CRAMFileFormat2-1-fig003.png img/CRAMFileFormat2-1-fig004.png img/CRAMFileFormat2-1-fig005.png img/CRAMFileFormat2-1-fig006.png img/CRAMFileFormat2-1-fig007.png -new/VCFv4.1.ver new/VCFv4.2.ver new/VCFv4.3.ver new/VCFv4.4.draft.ver: img/all_orientations-400x296.png img/derivation-400x267.png img/erosion-400x211.png img/inserted_contig-400x247.png img/inserted_sequence-400x189.png img/inversion-400x95.png img/microhomology-400x248.png img/multiple_mates-400x280.png img/phasing-400x259.png img/reciprocal_rearrangement-400x192.png img/telomere-400x251.png +new/VCFv4.1.ver new/VCFv4.2.ver new/VCFv4.3.ver new/VCFv4.4.ver: img/all_orientations-400x296.png img/derivation-400x267.png img/erosion-400x211.png img/inserted_contig-400x247.png img/inserted_sequence-400x189.png img/inversion-400x95.png img/microhomology-400x248.png img/multiple_mates-400x280.png img/phasing-400x259.png img/reciprocal_rearrangement-400x192.png img/telomere-400x251.png new/%.ver: %.tex | new scripts/genversion.sh $^ > $@ diff --git a/README.md b/README.md index 7b57ec04d..d8787524e 100644 --- a/README.md +++ b/README.md @@ -37,8 +37,7 @@ It has no formal definition and several incompatible variants, but is described Variant calling data files -------------------------- -**[VCFv4.3.tex]** is the canonical specification for the Variant Call Format and its textual (VCF) and binary (BCF) encodings, while **[VCFv4.1.tex]** and **[VCFv4.2.tex]** describe their predecessors. -**[VCFv4.4.draft.tex]** is a working draft of the upcoming version of VCF format and is under active revision. +**[VCFv4.4.tex]** is the canonical specification for the Variant Call Format and its textual (VCF) and binary (BCF) encodings, while **[VCFv4.1.tex]**, **[VCFv4.2.tex]** and **[VCFv4.3.tex]** describe their predecessors. These formats are discussed on the [vcftools-spec mailing list][vcfspec-ml]. **[BCFv1_qref.tex]** summarizes the obsolete BCF1 format historically produced by [samtools]. This format is no longer recommended for use, as it has been superseded by the more widely-implemented BCF2. @@ -74,7 +73,7 @@ Transfer protocols [VCFv4.1.tex]: http://samtools.github.io/hts-specs/VCFv4.1.pdf [VCFv4.2.tex]: http://samtools.github.io/hts-specs/VCFv4.2.pdf [VCFv4.3.tex]: http://samtools.github.io/hts-specs/VCFv4.3.pdf -[VCFv4.4.draft.tex]: http://samtools.github.io/hts-specs/VCFv4.4.draft.pdf +[VCFv4.4.tex]: http://samtools.github.io/hts-specs/VCFv4.4.pdf [BCFv1_qref.tex]: http://samtools.github.io/hts-specs/BCFv1_qref.pdf [BCFv2_qref.tex]: http://samtools.github.io/hts-specs/BCFv2_qref.pdf [BEDv1.tex]: https://samtools.github.io/hts-specs/BEDv1.pdf diff --git a/VCFv4.4.draft.pdf b/VCFv4.4.pdf similarity index 100% rename from VCFv4.4.draft.pdf rename to VCFv4.4.pdf diff --git a/VCFv4.4.draft.tex b/VCFv4.4.tex similarity index 99% rename from VCFv4.4.draft.tex rename to VCFv4.4.tex index 7a8a00c16..833ec9ff3 100644 --- a/VCFv4.4.draft.tex +++ b/VCFv4.4.tex @@ -7,11 +7,6 @@ \usepackage[margin=0.75in]{geometry} \usepackage[pdfborder={0 0 0}]{hyperref} -\usepackage{draftwatermark} -\SetWatermarkAngle{315} -\SetWatermarkText{PRELIMINARY} -\SetWatermarkScale{4} - \usepackage{listings} \lstset{ basicstyle=\ttfamily, @@ -22,8 +17,8 @@ \renewcommand{\thefootnote}{\fnsymbol{footnote}} \begin{document} -\input{VCFv4.4.draft.ver} -\title{\huge \color{red} DRAFT SPEC SUBJECT TO CHANGE \\ Release Candidate 2 \\ The Variant Call Format Specification \\ \vspace{0.5em} \large VCFv4.4 and BCFv2.2} +\input{VCFv4.4.ver} +\title{The Variant Call Format Specification \\ \vspace{0.5em} \large VCFv4.4 and BCFv2.2} \date{\headdate} \maketitle \begin{quote}\small diff --git a/index.md b/index.md index 2ff60cd1d..0c737cc34 100644 --- a/index.md +++ b/index.md @@ -24,7 +24,7 @@ Specifications: - [VCF v4.1](VCFv4.1.pdf) - [VCF v4.2](VCFv4.2.pdf) - [VCF v4.3](VCFv4.3.pdf) -- [VCF v4.4 draft](VCFv4.4.draft.pdf) +- [VCF v4.4](VCFv4.4.pdf) - [BED v1](BEDv1.pdf) - [crypt4gh](crypt4gh.pdf) - [Htsget](htsget.html)