From 4787a293e281502000caae21cf231fdd157eac25 Mon Sep 17 00:00:00 2001 From: Colin Date: Mon, 19 Dec 2022 10:42:38 -0700 Subject: [PATCH] Remove typos toml --- VCFv4.4.tex | 8 ++++---- _typos.toml | 6 ------ 2 files changed, 4 insertions(+), 10 deletions(-) delete mode 100644 _typos.toml diff --git a/VCFv4.4.tex b/VCFv4.4.tex index 055d5b9f9..b435e0e6d 100644 --- a/VCFv4.4.tex +++ b/VCFv4.4.tex @@ -607,12 +607,12 @@ \subsubsection{Genotype fields} \end{tabular} \item PSO (List of integers): List of phase set ordinals. - For each phase-set name, defines the order in which variants are encountered when traversing a derivate chromosome. + For each phase-set name, defines the order in which variants are encountered when traversing a derivative chromosome. The missing value '$.$' should be used when the corresponding PSO value is missing. For each phase-set name, PSO should be defined if any allele with that phase-set name on any record is symbolic structural variant or in breakpoint notation. Variants in breakpoint notation must have the same PSL and PSO on both records. - Without explicitly specifying the derivate chromosome traversal order, multiple derivate chromosome reconstructions are possible. + Without explicitly specifying the derivative chromosome traversal order, multiple derivative chromosome reconstructions are possible. Take for example this tandem duplication in a triploid organism with SNVs (ID/QUAL/FILTER columns removed for clarity): \vspace{0.5em} @@ -829,7 +829,7 @@ \section{INFO keys used for structural variants} \item BFB - breakage fusion bridge \item DOUBLEMINUTE - Double minute \end{itemize} -The sematics of other $EVENTTYPE$ values is implementation-defined. +The semantics of other $EVENTTYPE$ values is implementation-defined. The use of $EVENT$ is not restricted to structural variation and can also be used to associate non-symbolic alleles. Such linking is useful for scenarios such as kataegis or when there is variant position ambiguity in segmentally duplicated regions. @@ -2555,7 +2555,7 @@ \subsection{Changes between VCFv4.4 and VCFv4.3} \item Added tandem repeat support ($<$CNV:TR$>$, RN, RUS, RUL, RB, CIRB, RUC, CIRUC, RUB) \item Redefined INFO CN as allele-specific copy number and FORMAT CN as total copy number. \item Redefined INFO and FORMAT CN to support non-integer copy numbers. -\item Added support for phasing and derivate chromosome reconstruction in the presence of SVs (PSL, PSO, PSQ) +\item Added support for phasing and derivative chromosome reconstruction in the presence of SVs (PSL, PSO, PSQ) \item Added SVCLAIM to disambiguate copy number based $<$DEL$>$ and $<$DUP$>$ variants from breakpoint based ones. \item Conceptually separated variant detection and interpretation. \item Added EVENTTYPE/EVENT to enable the multiple records encoding complex genomic rearrangements to be grouped together. diff --git a/_typos.toml b/_typos.toml deleted file mode 100644 index afd027005..000000000 --- a/_typos.toml +++ /dev/null @@ -1,6 +0,0 @@ -[default.extend-words] -FO="FO" -BA="BA" -nd="nd" -Hsi="Hsi" -Apon="Apon"