X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcf.tex;h=6f2171fa56ee39c6d1baa23da8e18794764ddcb5;hp=5ca1e282020d640733b7a88be53db8d3a26a6220;hb=c34624801b980425af68c3c431423c72b18c14fe;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9

diff --git a/bcftools/bcf.tex b/bcftools/bcf.tex
index 5ca1e28..6f2171f 100644
--- a/bcftools/bcf.tex
+++ b/bcftools/bcf.tex
@@ -14,19 +14,19 @@
 \begin{tabular}{|l|l|l|l|l|}
 \hline
 \multicolumn{2}{|c|}{\bf Field} & \multicolumn{1}{c|}{\bf Descrption} & \multicolumn{1}{c|}{\bf Type} & \multicolumn{1}{c|}{\bf Value} \\\hline\hline
-\multicolumn{2}{|l|}{\tt magic} & Magic string & {\tt char[4]} & {\tt BCF\char92 4} \\\hline
-\multicolumn{2}{|l|}{\tt l\_nm} & Length of concatenated sequence names & {\tt int32\_t} & \\\hline
-\multicolumn{2}{|l|}{\tt name} & Concatenated names, {\tt NULL} padded & {\tt char[l\_nm]} & \\\hline
-\multicolumn{2}{|l|}{\tt l\_smpl} & Length of concatenated sample names & {\tt int32\_t} & \\\hline
-\multicolumn{2}{|l|}{\tt sname} & Concatenated sample names & {\tt char[l\_smpl]} & \\\hline
-\multicolumn{2}{|l|}{\tt l\_txt} & Length of the meta text (double-hash lines)& {\tt int32\_t} & \\\hline
-\multicolumn{2}{|l|}{\tt text} & Meta text, {\tt NULL} terminated & {\tt char[l\_txt]} & \\\hline
+\multicolumn{2}{|l|}{\sf magic} & Magic string & {\tt char[4]} & {\tt BCF\char92 4} \\\hline
+\multicolumn{2}{|l|}{\sf l\_seqnm} & Length of concatenated sequence names & {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf seqnm} & Concatenated names, {\tt NULL} padded & {\tt char[{\sf l\_seqnm}]} & \\\hline
+\multicolumn{2}{|l|}{\sf l\_smpl} & Length of concatenated sample names & {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf smpl} & Concatenated sample names & {\tt char[{\sf l\_smpl}]} & \\\hline
+\multicolumn{2}{|l|}{\sf l\_meta} & Length of the meta text (double-hash lines)& {\tt int32\_t} & \\\hline
+\multicolumn{2}{|l|}{\sf meta} & Meta text, {\tt NULL} terminated & {\tt char[{\sf l\_meta}]} & \\\hline
 \multicolumn{5}{|c|}{\it \color{gray}{List of records until the end of the file}}\\\cline{2-5}
-& {\tt seq\_id} & Reference sequence ID & {\tt int32\_t} & \\\cline{2-5}
-& {\tt pos} & Position & {\tt int32\_t} & \\\cline{2-5}
-& {\tt qual} & Variant quality & {\tt float} & \\\cline{2-5}
-& {\tt l\_str} & Length of str & {\tt int32\_t} & \\\cline{2-5}
-& {\tt str} & {\tt ID+REF+ALT+FILTER+INFO+FORMAT}, {\tt NULL} padded & {\tt char[slen]} &\\\cline{2-5}
+& {\sf seq\_id} & Reference sequence ID & {\tt int32\_t} & \\\cline{2-5}
+& {\sf pos} & Position & {\tt int32\_t} & \\\cline{2-5}
+& {\sf qual} & Variant quality & {\tt float} & \\\cline{2-5}
+& {\sf l\_str} & Length of {\sf str} & {\tt int32\_t} & \\\cline{2-5}
+& {\sf str} & {\tt ID+REF+ALT+FILTER+INFO+FORMAT}, {\tt NULL} padded & {\tt char[{\sf l\_str}]} &\\\cline{2-5}
 & \multicolumn{4}{c|}{Blocks of data; \#blocks and formats defined by {\tt FORMAT} (table below)}\\
 \hline
 \end{tabular}
@@ -37,27 +37,40 @@
 \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*x]} & Log10 likelihood of data; $x=\frac{m(m+1)}{2}$, $m=\#\{alleles\}$\\
-{\tt GT} & {\tt uint8\_t[n]} & {\tt phase\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
+{\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 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 $P$} \\
 {\tt GQ} & {\tt uint8\_t[n]} & {Genotype quality}\\
 {\tt HQ} & {\tt uint8\_t[n*2]} & {Haplotype quality}\\
-{\tt PL} & {\tt uint8\_t[n*x]} & {Phred-scaled likelihood of data}\\
-\emph{misc} & {\tt int32\_t+char*} & {\tt NULL} padded concatenated strings (integer equal to the length) \\
+{\tt \_HQ} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic HQ}\\
+{\tt IBD} & {\tt uint32\_t[n*2]} & {IBD}\\
+{\tt \_IBD} & {\tt uint8\_t+uint32\_t[n*P]} & {Generic IBD}\\
+{\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; $X$ 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}
 \end{center}
 
 \begin{itemize}
-\item The file is {\tt BGZF} compressed.
-\item All integers are little-endian.
+\item A BCF file is in the {\tt BGZF} format.
+\item All multi-byte numbers are little-endian.
 \item In a string, a missing value `.' is an empty C string ``{\tt
     \char92 0}'' (not ``{\tt .\char92 0}'')
 \item For {\tt GL} and {\tt PL}, likelihoods of genotypes appear in the
   order of alleles in {\tt REF} and then {\tt ALT}. For example, if {\tt
     REF=C}, {\tt ALT=T,A}, likelihoods appear in the order of {\tt
-    CC,CT,CA,TT,TA,AA}.
-\item {\tt GL} is an extension to and is backward compatible with the
-  {\tt GL} genotype field in {\tt VCFv4.0}.
+    CC,CT,TT,CA,TA,AA} (NB: the ordering is different from the one in the original
+	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.
 \end{itemize}
 
-\end{document}
\ No newline at end of file
+\end{document}