Commit d9b2388c authored by Laros's avatar Laros
Browse files

Added some figures.

parent b0d0334a
......@@ -23,26 +23,6 @@
\section{Introduction}
\makeTableOfContents
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.7\textheight]{gq}
\end{center}
\caption{}
\label{}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.7\textheight]{samples}
\end{center}
\caption{}
\label{}
\end{figure}
\end{pframe}
\subsection{Types of variants}
\begin{pframe}
% Data sharing at the LUMC:
......@@ -50,8 +30,6 @@
% - Variant frequencies.
\end{pframe}
% Issues with sharing frequencies:
% - See VKGL discussion.
\subsection{Requirements}
\begin{pframe}
We aim for a solution that has the following properties:
......@@ -73,6 +51,70 @@
Timestamps are essential for \emph{reproducibility}.
\end{pframe}
\begin{pframe}
\begin{figure}[]
\vspace{-0.5cm}
\begin{center}
\includegraphics[height=0.8\textheight]{gq}
\end{center}
\vspace{-0.3cm}
\caption{Callable region ($584$--$1596$).}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\vspace{-0.5cm}
\begin{center}
\includegraphics[height=0.8\textheight]{samples}
\begin{picture}(0, 0)
\only<2>{\put(-45, 9.5){\line(0, 1){50}}}
\only<3>{\put(-23, 9.5){\line(0, 1){50}}}
\end{picture}
\end{center}
\vspace{-0.3cm}
\caption{Sharing observations is not enough.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
\Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}
\end{center}
\caption{\bt{NM\_003002.2:c.262\_266del}.}
\end{figure}
\begin{figure}[]
\begin{center}
\Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}\\
\Large\texttt{TTGAATCCTT \color{red}GCTCT \color{black}GCGATGGA}\\
\Large\texttt{TTGAATCCTTG \color{red}CTCTG \color{black}CGATGGA}\\
\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
\end{center}
%\caption{\bt{NM\_003002.2:c.262\_266del}.}
\end{figure}
\begin{figure}[]
\begin{center}
\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
\end{center}
\caption{\bt{NM\_003002.2:c.265\_269del}.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
Genome\\
{\Large\texttt{AACTTAGGA \color{red}ACGAG \color{black}ACGCTACCT}}\\
{\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}}\\
Transcript
\end{center}
\caption{}
\end{figure}
\end{pframe}
\subsection{Options}
\begin{pframe}
Choices for the database layout:
......
#!/bin/sh
python gq.py '[(500, 1500)]' > gq_1.dat
python gq.py '[(100, 600), (1000, 1600)]' > gq_2.dat
python gq.py '[(1200, 1800)]' > gq_3.dat
......@@ -8,4 +8,4 @@ set multiplot
set nokey
plot "gq_1.dat" notitle
set style data lines
plot 30 lc 0 lw 8
plot 30 lc 0 lw 10
#!/usr/bin/env python
import random
import sys
coverage = eval(sys.argv[1])
def target_coverage(position, coverage):
for c in coverage:
if c[0] <= position <= c[1]:
return 45
return 0
y = 0
for i in range(2000):
y = max(0, y + random.randint(-1, 1))
for x in range(2000):
dy = random.randint(-1, 1)
t = target_coverage(x, coverage)
if not random.randint(0, 1):
if y > t + 5:
dy = min(0, dy)
if y < t - 5:
dy = max(0, dy)
y = max(0, y + dy)
print y
0
0
0
1
2
1
0
0
0
0
1
0
0
0
0
1
1
1
2
2
3
4
5
5
6
6
5
6
6
5
4
3
4
4
4
4
3
3
2
3
2
3
3
2
2
2
3
2
1
2
3
3
4
4
5
5
4
4
3
3
3
3
2
1
2
1
2
1
1
2
1
1
0
1
1
2
3
3
2
3
4
3
4
5
5
4
5
5
5
6
5
4
5
6
7
8
7
8
7
6
8
8
8
7
7
7
6
6
5
5
5
5
5
4
5
5
6
5
6
5
5
6
5
6
6
6
7
7
7
7
8
8
8
7
7
6
7
7
8
8
8
7
7
7
6
6
6
6
6
6
5
5
4
5
5
4
4
4
3
3
4
5
5
6
6
5
5
5
4
4
5
6
6
6
6
6
6
7
6
5
6
7
7
7
8
8
8
9
9
9
9
8
8
7
7
7
6
6
7
7
7
6
6
7
8
8
7
6
5
4
3
2
2
1
1
2
2
3
2
2
3
4
5
5
5
6
5
6
6
5
6
5
5
6
7
8
9
10
10
11
11
12
12
13
12
12
13
12
12
13
12
13
13
12
12
12
12
12
12
11
12
13
14
14
14
15
15
16
17
18
19
19
20
19
20
21
21
22
22
21
21
20
19
18
17
17
16
15
16
15
16
15
15
15
16
16
15
14
14
15
15
16
15
15
15
14
14
14
15
14
14
15
15
16
15
16
16
16
16
17
17
17
16
17
18
18
18
17
18
17
17
16
17
17
17
17
16
17
18
18
18
18
18
19
20
19
18
18
19
19
20
21
20
21
20
20
21
20
21
22
22
23
24
25
25
25
25
24
25
26
27
27
28
29
28
29
30
31
30
30
30
31
32
31
31
32
32
33
34
33
33
33
32
31
30
31
30
31
30
30
31
30
30
31
32
33
32
32
31
31
31
32
33
34
33
34
33
33
33
33
33
34
33
32
33
34
35
34
33
34
35
34
33
34
33
34
34
34
35
35
36
35
35
35
35
34
34
35
36
35
34
35
36
36
37
38
37
38
37
36
35
36
36
35
35
34
35
36
35
36
36
35
35
34
34
35
34
33
34
33
32
33
32
31
30
31
31
32
33
34
34
34
34
34
33
34
33