1#!/bin/sh
2#
3# Currently, we run RazerS only on
4
5# We use revision 13816 for building the gold standard.
6RAZERS=${RAZERS:-../../../../../seqan-trunk-build/release/bin/razers3}
7
8for tc in 0 1; do  # number of threads, 0 and >0 have different code paths
9
10# ============================================================
11# Run Adeno Single-End Example
12# ============================================================
13
14for rl in 36 100; do
15    # Run with defaults for everything.
16    ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-tc${tc}.razers > se-adeno-reads${rl}_1-tc${tc}.stdout
17
18    # No gaps.
19    ${RAZERS} -tc ${tc} --no-gaps adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-ng-tc${tc}.razers > se-adeno-reads${rl}_1-ng-tc${tc}.stdout
20
21    # Compute forward/reverse maches only.
22    ${RAZERS} -tc ${tc} -f adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-f-tc${tc}.razers > se-adeno-reads${rl}_1-f-tc${tc}.stdout
23    ${RAZERS} -tc ${tc} -r adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-r-tc${tc}.razers > se-adeno-reads${rl}_1-r-tc${tc}.stdout
24
25    # Compute with different identity rates.
26    for i in 90 91 92 93 94 95 96 97 98 99 100; do
27        ${RAZERS} -tc ${tc} -i ${i} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-i${i}-tc${tc}.razers > se-adeno-reads${rl}_1-i${i}-tc${tc}.stdout
28    done
29
30    # Run with different output formats.
31    for pair in 0.razers 1.fa 2.eland 3.gff 4.sam 5.afg; do
32        of=$(echo $pair | sed 's/\..*$//g')
33        suffix=$(echo $pair | sed 's/^.\.//g')
34        ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-of${of}-tc${tc}.${suffix} > se-adeno-reads${rl}_1-of${of}-tc${tc}.stdout
35    done
36
37    # Run with different match ordering.
38    for so in 0 1; do
39        ${RAZERS} -tc ${tc} -so ${so} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-so${so}-tc${tc}.razers > se-adeno-reads${rl}_1-so${so}-tc${tc}.stdout
40    done
41done
42
43# ============================================================
44# Run Adeno Paired-End Example
45# ============================================================
46
47for rl in 36 100; do
48    # Run with defaults for everything.
49    ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-tc${tc}.razers > pe-adeno-reads${rl}_2-tc${tc}.stdout
50
51    # Allow indels.
52    ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-tc${tc}.razers > pe-adeno-reads${rl}_2-tc${tc}.stdout
53
54    # Compute forward/backward maches only.
55    ${RAZERS} -tc ${tc} -f adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-f-tc${tc}.razers > pe-adeno-reads${rl}_2-f-tc${tc}.stdout
56    ${RAZERS} -tc ${tc} -r adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-r-tc${tc}.razers > pe-adeno-reads${rl}_2-r-tc${tc}.stdout
57
58    # Compute with different identity rates.
59    for i in 90 91 92 93 94 95 96 97 98 99 100; do
60        ${RAZERS} -tc ${tc} -i ${i} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-i${i}-tc${tc}.razers > pe-adeno-reads${rl}_2-i${i}-tc${tc}.stdout
61    done
62
63    # Run with different output formats.
64    for pair in 0.razers 1.fa 2.eland 3.gff 4.sam 5.afg; do
65        of=$(echo $pair | sed 's/\..*$//g')
66        suffix=$(echo $pair | sed 's/^.\.//g')
67        ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-of${of}-tc${tc}.${suffix} > pe-adeno-reads${rl}_2-of${of}-tc${tc}.stdout
68    done
69
70    # Run with different match ordering.
71    for so in 0 1; do
72        ${RAZERS} -tc ${tc} -so ${so} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-so${so}-tc${tc}.razers > pe-adeno-reads${rl}_2-so${so}-tc${tc}.stdout
73    done
74done
75
76done  # for nt
77