From be23aaa60686ac4bfae404b635cfd70f5045ba6d Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Tue, 1 Oct 2024 11:36:56 +1300
Subject: [PATCH] Set off example tabular environment with the usual spacing
 [formatting]

---
 VCFv4.5.tex | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/VCFv4.5.tex b/VCFv4.5.tex
index e288aa94..0530513b 100644
--- a/VCFv4.5.tex
+++ b/VCFv4.5.tex
@@ -696,6 +696,8 @@ \subsubsection{Genotype fields}
   For example, if REF is G, ALT is A,C,T,\verb!<*>! and a genotype only has information about G, C, and \verb!<*>!, one can have LAA=[2,4] and thus LPL will be interpreted as pertaining to the alleles [G, C, \verb!<*>!] and not contain likelihood values for genotypes that involve A or T.
   GQ is still the genotype quality, even when the genotype is given against the local alleles.
   In the following example, the records with the same POS encode the same information (some columns removed for clarity):
+
+  \vspace{0.5em}
   \begin{tabular}[l]{llllll}
   	POS &REF&  ALT&FORMAT&sample\\
   	1&G&A,C,T,\textless*\textgreater& GT:LAA:LAD:LPL&  2/4:2,4:20,30,10:90,80,0,100,110,120\\
@@ -707,6 +709,7 @@ \subsubsection{Genotype fields}
   	4&G&A,T,\textless*\textgreater& GT:LAA:LAD:LPL& 0/0::30:0\\
   	4&G&A,T,\textless*\textgreater& GT:AD:PL& 0/0:30,.,.,.:0,.,.,.,.,.,.,.,.,.\\
   \end{tabular}
+
   Due to BCF encoding empty vectors as missing, implementation-defined Number=LA local-allele fields should not be used if distinguishing between zero-length data and missing data is required at REF-only sites.
   
   It is recommended that VCF libraries provide an API in which local allele encoding can be abstracted away from the API consumer and values accessed through their corresponding non-local key.