Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded...

[samtools.git] / bcftools / bcf.tex

diff --git a/bcftools/bcf.tex b/bcftools/bcf.tex
index 53bb8b022a27269c60fa1c353bfd65fe45337905..442fc2a0186ab03d66a055c404fea6cdcef632c1 100644 (file)
--- a/bcftools/bcf.tex
+++ b/bcftools/bcf.tex
@@ -33,13 +33,14 @@
 \end{center}
 
 \begin{center}
-\begin{tabular}{cll}
+\begin{tabular}{clp{9cm}}
 \hline
 \multicolumn{1}{l}{\bf Field} & \multicolumn{1}{l}{\bf Type} & \multicolumn{1}{l}{\bf Description} \\\hline
 {\tt DP} & {\tt uint16\_t[n]} & Read depth \\
 {\tt GL} & {\tt float[n*G]} & Log10 likelihood of data; $G=\frac{A(A+1)}{2}$, $A=\#\{alleles\}$\\
-{\tt GT} & {\tt uint8\_t[n]} & {\tt haploid\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
-{\tt \_GT} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic GT; the first int equals the max ploidy $P$} \\
+{\tt GT} & {\tt uint8\_t[n]} & {\tt missing\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
+{\tt \_GT} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic GT; the first int equals the max ploidy $P$. If the highest bit is set,
+       the allele is not present (e.g. due to different ploidy between samples).} \\
 {\tt GQ} & {\tt uint8\_t[n]} & {Genotype quality}\\
 {\tt HQ} & {\tt uint8\_t[n*2]} & {Haplotype quality}\\
 {\tt \_HQ} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic HQ}\\
@@ -48,8 +49,8 @@
 {\tt PL} & {\tt uint8\_t[n*G]} & {Phred-scaled likelihood of data}\\
 {\tt PS} & {\tt uint32\_t[n]} & {Phase set}\\
 %{\tt SP} & {\tt uint8\_t[n]} & {Strand bias P-value (bcftools only)}\\
-\emph{Integer} & {\tt int32\_t[n*X]} & {Fix-sized custom Integer; $X$ can be $1$, $A$ or $G$.}\\
-\emph{Numeric} & {\tt double[n*X]} & {Fix-sized custom Numeric; $X$ can be $1$, $A$ or $G$.}\\
+\emph{Integer} & {\tt int32\_t[n*X]} & {Fix-sized custom Integer; $X$ defined in the header}\\
+\emph{Numeric} & {\tt double[n*X]} & {Fix-sized custom Numeric}\\
 \emph{String} & {\tt uint32\_t+char*} & {\tt NULL} padded concat. strings (int equals to the length) \\
 \hline
 \end{tabular}
@@ -67,10 +68,10 @@
        BCF proposal).
 \item Predefined {\tt FORMAT} fields can be missing from VCF headers, but custom {\tt FORMAT} fields
        are required to be explicitly defined in the headers.
-\item A {\tt FORMAT} field with its name starting with `{\tt \_}' gives an alternative
-       binary representation of the corresponding VCF field. The alternative representation
-       is used when the default representation is unable to keep the genotype information,
-       for example, when the ploidy is over 2 or there are more than 8 alleles.
+\item A {\tt FORMAT} field with its name starting with `{\tt \_}' is specific to BCF only.
+       It gives an alternative binary representation of the corresponding VCF field, in case
+       the default representation is unable to keep the genotype information,
+       for example, when the ploidy is not 2 or there are more than 8 alleles.
 \end{itemize}
 
 \end{document}