From 958f3731a3c28a3aad23826eda156c01bdec54ea Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Thu, 30 May 2019 10:52:09 -0400 Subject: [PATCH 1/4] draft of sample ID and filter update --- VCFv4.2.tex | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/VCFv4.2.tex b/VCFv4.2.tex index 01e40bc98..1935e0655 100644 --- a/VCFv4.2.tex +++ b/VCFv4.2.tex @@ -141,9 +141,12 @@ \subsubsection{Sample field format} It is possible to define sample to genome mappings as shown below: \small \begin{verbatim} -##SAMPLE= +##SAMPLE= \end{verbatim} \normalsize +ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (',') character. +FILTER is a string that has been defined in a ##FILTER line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). + \subsubsection{Pedigree field format} It is possible to record relationships between genomes using the following syntax: \begin{verbatim} From ae2612a270552e32302b390a7162f6c17780967a Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Wed, 24 Jul 2019 16:59:46 -0400 Subject: [PATCH 2/4] fixing build error --- VCFv4.2.tex | 2 +- VCFv4.3.tex | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/VCFv4.2.tex b/VCFv4.2.tex index 1935e0655..61dd055c1 100644 --- a/VCFv4.2.tex +++ b/VCFv4.2.tex @@ -145,7 +145,7 @@ \subsubsection{Sample field format} \end{verbatim} \normalsize ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (',') character. -FILTER is a string that has been defined in a ##FILTER line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). +FILTER is a string that has been defined in a \verb!##FILTER\verb! line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). \subsubsection{Pedigree field format} It is possible to record relationships between genomes using the following syntax: diff --git a/VCFv4.3.tex b/VCFv4.3.tex index e9e2c7301..8a6a5c878 100644 --- a/VCFv4.3.tex +++ b/VCFv4.3.tex @@ -240,6 +240,12 @@ \subsubsection{Sample field format} ##SAMPLE= \end{verbatim}} +In the \verb!SAMPLE! line: +\begin{itemize} +\item{ID} is a string that identifies the sample. It comprises non-whitespace characters and doesn't include the comma (',') character. +\item{FILTER} is a string that has been defined in a \verb!##FILTER\verb! line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). +\end{itemize} + \subsubsection{Pedigree field format} It is possible to record relationships between genomes using the following syntax: \begin{verbatim} From 6369341fde160a9b9b5b29e0b4ba05c1a29c1dc0 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Wed, 24 Jul 2019 17:05:18 -0400 Subject: [PATCH 3/4] oops --- VCFv4.2.tex | 4 ++-- VCFv4.3.tex | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/VCFv4.2.tex b/VCFv4.2.tex index 61dd055c1..563cfac64 100644 --- a/VCFv4.2.tex +++ b/VCFv4.2.tex @@ -144,8 +144,8 @@ \subsubsection{Sample field format} ##SAMPLE= \end{verbatim} \normalsize -ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (',') character. -FILTER is a string that has been defined in a \verb!##FILTER\verb! line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). +ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (`,') character. +FILTER is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). \subsubsection{Pedigree field format} It is possible to record relationships between genomes using the following syntax: diff --git a/VCFv4.3.tex b/VCFv4.3.tex index 8a6a5c878..1a2f7d954 100644 --- a/VCFv4.3.tex +++ b/VCFv4.3.tex @@ -242,8 +242,9 @@ \subsubsection{Sample field format} In the \verb!SAMPLE! line: \begin{itemize} -\item{ID} is a string that identifies the sample. It comprises non-whitespace characters and doesn't include the comma (',') character. -\item{FILTER} is a string that has been defined in a \verb!##FILTER\verb! line, except for PASS or '.' which mean that the sample passes or that the filter is missing (respectively). +\item{ID} is a string that identifies the sample. +It comprises non-whitespace characters and doesn't include the comma (`.') character. +\item{FILTER} is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). \end{itemize} \subsubsection{Pedigree field format} From aaadf53ce102fe9981ad34f8f0c9bdaa5faf99b1 Mon Sep 17 00:00:00 2001 From: Yossi Farjoun Date: Wed, 24 Jul 2019 17:09:45 -0400 Subject: [PATCH 4/4] spaces --- VCFv4.2.tex | 2 +- VCFv4.3.tex | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/VCFv4.2.tex b/VCFv4.2.tex index 563cfac64..2469d7830 100644 --- a/VCFv4.2.tex +++ b/VCFv4.2.tex @@ -145,7 +145,7 @@ \subsubsection{Sample field format} \end{verbatim} \normalsize ID is a string that identifies the sample. It comprises of non-whitespace characters and doesn't include the comma (`,') character. -FILTER is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). +FILTER is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). \subsubsection{Pedigree field format} It is possible to record relationships between genomes using the following syntax: diff --git a/VCFv4.3.tex b/VCFv4.3.tex index 1a2f7d954..8e7ce61ab 100644 --- a/VCFv4.3.tex +++ b/VCFv4.3.tex @@ -244,7 +244,7 @@ \subsubsection{Sample field format} \begin{itemize} \item{ID} is a string that identifies the sample. It comprises non-whitespace characters and doesn't include the comma (`.') character. -\item{FILTER} is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). +\item{FILTER} is a string that has been defined in a \verb!##FILTER! line, except for PASS or `.' which mean that the sample passes or that the filter is missing (respectively). \end{itemize} \subsubsection{Pedigree field format}