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Merged
cyenyxe merged 8 commits into from
Mar 8, 2019
Merged

Miscellaneous VCF formatting and typo fixes #391

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905d0f7
Fix typos in BCF encoding example
jmarshall Feb 25, 2019
08ba7d9
Use a less goofy example string
jmarshall Mar 2, 2019
84e7e28
Use TeX ``quote marks'' --- and dashes
jmarshall Mar 2, 2019
b61597e
Improve positioning of SV figures
jmarshall Mar 2, 2019
129fdd5
Avoid end-of-sentence spacing after i.e. and e.g.
jmarshall Mar 4, 2019
c6bf7a8
Improve positioning of "Reserved INFO/genotype keys" tables
jmarshall Mar 5, 2019
c8c55da
Improve a couple of page breaks
jmarshall Mar 5, 2019
be61055
Fix DPADJ delimiter: comma, not vertical bar
jmarshall Mar 7, 2019
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28 changes: 14 additions & 14 deletions VCFv4.1.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -831,10 +831,10 @@ \subsubsection{Sample mixtures}
\begin{flushleft}
\begin{tabular}{ l l l l l l l l l l l }
\#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Blood & TissueSample\\
2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_U & GT:DPADJ & 0:32 & $0\mid1:9\mid21$ \\
2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & SVTYPE=BND;MATEID=bnd\_X & GT:DPADJ & 0:29 & $0\mid1:11\mid25$ \\
13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_W & GT:DPADJ & 0:34 & $0\mid1:10\mid23$ \\
13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & SVTYPE=BND;MATEID=bnd\_V & GT:DPADJ & 0:31 & $0\mid1:8\mid20$ \\
2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_U & GT:DPADJ & 0:32 & $0|1:9,21$ \\
2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & SVTYPE=BND;MATEID=bnd\_X & GT:DPADJ & 0:29 & $0|1:11,25$ \\
13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_W & GT:DPADJ & 0:34 & $0|1:10,23$ \\
13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & SVTYPE=BND;MATEID=bnd\_V & GT:DPADJ & 0:31 & $0|1:8,20$ \\
\end{tabular}
\end{flushleft}
\normalsize
Expand Down Expand Up @@ -1186,21 +1186,21 @@ \subsubsection{Type encoding}
\vspace{0.3cm}
\textbf{String} values have two basic encodings. For INFO, FORMAT, and FILTER keys these are encoded by integer offsets into the header dictionary. For string values, such as found in the ID, REF, ALT, INFO, and FORMAT fields, strings are encoded as typed array of ASCII encoded bytes. The array isn't terminated by a null byte. The length of the string is given by the length of the type descriptor.

Suppose you want to encode the string ACAC. First, we need the type descriptor byte, which is the string type 0x07 or'd with inline size (4) yielding the type byte of 0x40 | 0x07 = 0x47. Immediately following the type byte is the four byte ASCII encoding of ``ACAC'' 0x41 0x43 0x41 0x43. So the final encoding is:
Suppose you want to encode the string ``{\tt ACAC}''. First, we need the type descriptor byte, which is the string type 0x07 or'd with inline size (4) yielding the type byte of 0x40 $|$ 0x07 = 0x47. Immediately following the type byte is the four byte ASCII encoding of ``{\tt ACAC}'': 0x41 0x43 0x41 0x43. So the final encoding is:

\vspace{0.1cm}
\begin{tabular}{| l | l |} \hline
0x47 0x41 0x43 0x41 0x43 & String type with inline size of 4 followed by ACAC in ASCII \\ \hline
\end{tabular}
\vspace{0.3cm}

Suppose you want to encode the string MarkDePristoWorksAtTheBroad, a string of size 27. First, we need the type descriptor byte, which is the string type 0x07. Because the size exceeds the inline size ($27 > 15$) we set the size to overflow, yielding the type byte of 0xF0 | 0x07 = 0xF7. Immediately following the type byte is the typed size of 27, which we encode by the atomic INT8 value: 0x11 followed by the actual size 0x1B. Finally comes the actual bytes of the string: 0x4D 0x61 0x72 0x6B 0x44 0x65 0x50 0x72 0x69 0x73 0x74 0x6F 0x57 0x6F 0x72 0x6B 0x73 0x41 0x74 0x54 0x68 0x65 0x42 0x72 0x6F 0x61 0x64. So the final encoding is:
Suppose you want to encode the string ``{\tt VariantCallFormatSampleText}'', a string of size 27. First, we need the type descriptor byte, which is the string type 0x07. Because the size exceeds the inline size limit ($27 \geq 15$) we set the size to overflow, yielding the type byte of 0xF0 $|$ 0x07 = 0xF7. Immediately following the type byte is the typed size of 27, which we encode by the atomic INT8 value: 0x11 followed by the actual size 0x1B. Finally comes the actual bytes of the string: 0x56 0x61 0x72 0x69 0x61 0x6E 0x74 0x43 0x61 0x6C 0x6C 0x46 0x6F 0x72 0x6D 0x61 0x74 0x53 0x61 0x6D 0x70 0x6C 0x65 0x54 0x65 0x78 0x74. So the final encoding is:

\vspace{0.3cm}
\begin{tabular}{ | p{9cm} | p{6cm} | } \hline
0xF7 & string with overflow size \\ \hline
0x11 0x1B & overflow size encoded as INT8 with value 27 \\ \hline
0x4D 0x61 0x72 0x6B 0x44 0x65 0x50 0x72 0x69 0x73 0x74 0x6F 0x57 0x6F 0x72 0x6B 0x73 0x41 0x74 0x54 0x68 0x65 0x42 0x72 0x6F 0x61 0x64 & message in ASCII \\ \hline
0x56 0x61 0x72 0x69 0x61 0x6E 0x74 0x43 0x61 0x6C 0x6C 0x46 0x6F 0x72 0x6D 0x61 0x74 0x53 0x61 0x6D 0x70 0x6C 0x65 0x54 0x65 0x78 0x74 & message in ASCII \\ \hline
\end{tabular}
\vspace{0.3cm}

Expand Down Expand Up @@ -1320,13 +1320,13 @@ \subsubsection{Encoding QUAL}

\subsubsection{Encoding ID}

For ID type byte would is a 5-element string (type descriptor 0x59),
For ID type byte would is a 5-element string (type descriptor 0x57),
which would then be followed by the five bytes for the string of
{\tt 0x72 0x73 0x31 0x32 0x33}. The full encoding is:

\vspace{0.3cm}
\begin{tabular}{|l| l|} \hline
0x59 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x57 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
\end{tabular}

\subsubsection{Encoding REF/ALT fields}
Expand Down Expand Up @@ -1381,7 +1381,7 @@ \subsubsection{Encoding the INFO fields}

\vspace{0.3cm}
\begin{tabular}{|l |l|} \hline
0x11 0x51 & AA key \\ \hline
0x11 0x53 & AA key \\ \hline
0x17 0x43 & with value of C \\ \hline
\end{tabular}

Expand Down Expand Up @@ -1425,7 +1425,7 @@ \subsubsection{Encoding Genotypes}

We need to determine a few values before writing out the final block:

l\_shared = 54 (Data length from CHROM to the end of INFO)
l\_shared = 52 (Data length from CHROM to the end of INFO)

l\_indiv = 42 (Data length of FORMAT and individual genotype fields)

Expand All @@ -1436,15 +1436,15 @@ \subsubsection{Encoding Genotypes}

\vspace{0.3cm}
\begin{tabular}{|l| l|} \hline
0x36000000 & l\_shared as little endian hex \\ \hline
0x34000000 & l\_shared as little endian hex \\ \hline
0x2A000000 & l\_indiv as little endian hex \\ \hline
0x01000000 & CHROM offset is at 1 in 32 bit little endian \\ \hline
0x64000000 & POS in 0 base 32 bit little endian \\ \hline
0x01000000 & rlen = 1 (it's just a SNP) \\ \hline
0x41 0xF0 0xCC 0xCD & QUAL = 30.1 as 32-bit float \\ \hline
0x00020004 & n\_allele\_info \\ \hline
0x05000003 & n\_fmt\_samples \\ \hline
0x59 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x57 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x17 0x41 & REF A \\ \hline
0x17 0x43 & ALT C \\ \hline
0x11 0x00 & FILTER field PASS \\ \hline
Expand All @@ -1453,7 +1453,7 @@ \subsubsection{Encoding Genotypes}
0x11 0x03 & with value of 3 \\ \hline
0x11 0x52 & AN key \\ \hline
0x11 0x06 & with value of 6 \\ \hline
0x11 0x51 & AA key \\ \hline
0x11 0x53 & AA key \\ \hline
0x17 0x43 & with value of C \\ \hline
0x1101 0x21 0x020202040404 & GT \\ \hline
0x1102 0x11 0x0A0A0A & GQ \\ \hline
Expand Down
28 changes: 14 additions & 14 deletions VCFv4.2.tex
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -848,10 +848,10 @@ \subsubsection{Sample mixtures}
\begin{flushleft}
\begin{tabular}{ l l l l l l l l l l l }
\#CHROM & POS & ID & REF & ALT & QUAL & FILTER & INFO & FORMAT & Blood & TissueSample\\
2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_U & GT:DPADJ & 0:32 & $0\mid1:9\mid21$ \\
2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & SVTYPE=BND;MATEID=bnd\_X & GT:DPADJ & 0:29 & $0\mid1:11\mid25$ \\
13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_W & GT:DPADJ & 0:34 & $0\mid1:10\mid23$ \\
13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & SVTYPE=BND;MATEID=bnd\_V & GT:DPADJ & 0:31 & $0\mid1:8\mid20$ \\
2 & 321681 & bnd\_W & G & G$]2:421681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_U & GT:DPADJ & 0:32 & $0|1:9,21$ \\
2 & 321682 & bnd\_V & T & $[2:421682[$T & 6 & PASS & SVTYPE=BND;MATEID=bnd\_X & GT:DPADJ & 0:29 & $0|1:11,25$ \\
13 & 421681 & bnd\_U & A & A$]2:321681]$ & 6 & PASS & SVTYPE=BND;MATEID=bnd\_W & GT:DPADJ & 0:34 & $0|1:10,23$ \\
13 & 421682 & bnd\_X & C & $[2:321682[$C & 6 & PASS & SVTYPE=BND;MATEID=bnd\_V & GT:DPADJ & 0:31 & $0|1:8,20$ \\
\end{tabular}
\end{flushleft}
\normalsize
Expand Down Expand Up @@ -1203,21 +1203,21 @@ \subsubsection{Type encoding}
\vspace{0.3cm}
\textbf{String} values have two basic encodings. For INFO, FORMAT, and FILTER keys these are encoded by integer offsets into the header dictionary. For string values, such as found in the ID, REF, ALT, INFO, and FORMAT fields, strings are encoded as typed array of ASCII encoded bytes. The array isn't terminated by a null byte. The length of the string is given by the length of the type descriptor.

Suppose you want to encode the string ACAC. First, we need the type descriptor byte, which is the string type 0x07 or'd with inline size (4) yielding the type byte of 0x40 | 0x07 = 0x47. Immediately following the type byte is the four byte ASCII encoding of ``ACAC'' 0x41 0x43 0x41 0x43. So the final encoding is:
Suppose you want to encode the string ``{\tt ACAC}''. First, we need the type descriptor byte, which is the string type 0x07 or'd with inline size (4) yielding the type byte of 0x40 $|$ 0x07 = 0x47. Immediately following the type byte is the four byte ASCII encoding of ``{\tt ACAC}'': 0x41 0x43 0x41 0x43. So the final encoding is:

\vspace{0.1cm}
\begin{tabular}{| l | l |} \hline
0x47 0x41 0x43 0x41 0x43 & String type with inline size of 4 followed by ACAC in ASCII \\ \hline
\end{tabular}
\vspace{0.3cm}

Suppose you want to encode the string MarkDePristoWorksAtTheBroad, a string of size 27. First, we need the type descriptor byte, which is the string type 0x07. Because the size exceeds the inline size ($27 > 15$) we set the size to overflow, yielding the type byte of 0xF0 | 0x07 = 0xF7. Immediately following the type byte is the typed size of 27, which we encode by the atomic INT8 value: 0x11 followed by the actual size 0x1B. Finally comes the actual bytes of the string: 0x4D 0x61 0x72 0x6B 0x44 0x65 0x50 0x72 0x69 0x73 0x74 0x6F 0x57 0x6F 0x72 0x6B 0x73 0x41 0x74 0x54 0x68 0x65 0x42 0x72 0x6F 0x61 0x64. So the final encoding is:
Suppose you want to encode the string ``{\tt VariantCallFormatSampleText}'', a string of size 27. First, we need the type descriptor byte, which is the string type 0x07. Because the size exceeds the inline size limit ($27 \geq 15$) we set the size to overflow, yielding the type byte of 0xF0 $|$ 0x07 = 0xF7. Immediately following the type byte is the typed size of 27, which we encode by the atomic INT8 value: 0x11 followed by the actual size 0x1B. Finally comes the actual bytes of the string: 0x56 0x61 0x72 0x69 0x61 0x6E 0x74 0x43 0x61 0x6C 0x6C 0x46 0x6F 0x72 0x6D 0x61 0x74 0x53 0x61 0x6D 0x70 0x6C 0x65 0x54 0x65 0x78 0x74. So the final encoding is:

\vspace{0.3cm}
\begin{tabular}{ | p{9cm} | p{6cm} | } \hline
0xF7 & string with overflow size \\ \hline
0x11 0x1B & overflow size encoded as INT8 with value 27 \\ \hline
0x4D 0x61 0x72 0x6B 0x44 0x65 0x50 0x72 0x69 0x73 0x74 0x6F 0x57 0x6F 0x72 0x6B 0x73 0x41 0x74 0x54 0x68 0x65 0x42 0x72 0x6F 0x61 0x64 & message in ASCII \\ \hline
0x56 0x61 0x72 0x69 0x61 0x6E 0x74 0x43 0x61 0x6C 0x6C 0x46 0x6F 0x72 0x6D 0x61 0x74 0x53 0x61 0x6D 0x70 0x6C 0x65 0x54 0x65 0x78 0x74 & message in ASCII \\ \hline
\end{tabular}
\vspace{0.3cm}

Expand Down Expand Up @@ -1337,13 +1337,13 @@ \subsubsection{Encoding QUAL}

\subsubsection{Encoding ID}

For ID type byte would is a 5-element string (type descriptor 0x59),
For ID type byte would is a 5-element string (type descriptor 0x57),
which would then be followed by the five bytes for the string of
{\tt 0x72 0x73 0x31 0x32 0x33}. The full encoding is:

\vspace{0.3cm}
\begin{tabular}{|l| l|} \hline
0x59 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x57 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
\end{tabular}

\subsubsection{Encoding REF/ALT fields}
Expand Down Expand Up @@ -1398,7 +1398,7 @@ \subsubsection{Encoding the INFO fields}

\vspace{0.3cm}
\begin{tabular}{|l |l|} \hline
0x11 0x51 & AA key \\ \hline
0x11 0x53 & AA key \\ \hline
0x17 0x43 & with value of C \\ \hline
\end{tabular}

Expand Down Expand Up @@ -1442,7 +1442,7 @@ \subsubsection{Encoding Genotypes}

We need to determine a few values before writing out the final block:

l\_shared = 54 (Data length from CHROM to the end of INFO)
l\_shared = 52 (Data length from CHROM to the end of INFO)

l\_indiv = 42 (Data length of FORMAT and individual genotype fields)

Expand All @@ -1453,15 +1453,15 @@ \subsubsection{Encoding Genotypes}

\vspace{0.3cm}
\begin{tabular}{|l| l|} \hline
0x36000000 & l\_shared as little endian hex \\ \hline
0x34000000 & l\_shared as little endian hex \\ \hline
0x2A000000 & l\_indiv as little endian hex \\ \hline
0x01000000 & CHROM offset is at 1 in 32 bit little endian \\ \hline
0x64000000 & POS in 0 base 32 bit little endian \\ \hline
0x01000000 & rlen = 1 (it's just a SNP) \\ \hline
0x41 0xF0 0xCC 0xCD & QUAL = 30.1 as 32-bit float \\ \hline
0x00020004 & n\_allele\_info \\ \hline
0x05000003 & n\_fmt\_samples \\ \hline
0x59 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x57 0x72 0x73 0x31 0x32 0x33 & ID \\ \hline
0x17 0x41 & REF A \\ \hline
0x17 0x43 & ALT C \\ \hline
0x11 0x00 & FILTER field PASS \\ \hline
Expand All @@ -1470,7 +1470,7 @@ \subsubsection{Encoding Genotypes}
0x11 0x03 & with value of 3 \\ \hline
0x11 0x52 & AN key \\ \hline
0x11 0x06 & with value of 6 \\ \hline
0x11 0x51 & AA key \\ \hline
0x11 0x53 & AA key \\ \hline
0x17 0x43 & with value of C \\ \hline
0x1101 0x21 0x020202040404 & GT \\ \hline
0x1102 0x11 0x0A0A0A & GQ \\ \hline
Expand Down
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