1#!/bin/sh
2#
3# Expected output generation for rabema.
4
5# We use the current trunk version of 2011-10-13 (r10463) for building the
6# reference.
7RAZERS=../../../../build/Release/apps/razers2/razers2
8RABEMA_PREPARE=../../../../build/Release/apps/rabema/rabema_prepare_sam
9RABEMA_BUILD=../../../../build/Release/apps/rabema/rabema_build_gold_standard
10RABEMA_EVALUATE=../../../../build/Release/apps/rabema/rabema_evaluate
11
12# ============================================================
13# Map reads for gold standard and with too low error rate.
14# ============================================================
15
16${RAZERS} -m 10000 -vv -of 4 -ds -i 92     -o gold-adeno-hamming-08.sam adeno-genome.fa reads.fasta
17${RAZERS} -m 10000 -vv -of 4 -ds -i 92 -id -o gold-adeno-edit-08.sam    adeno-genome.fa reads.fasta
18
19${RAZERS} -vv -of 4 -ds -i 92     -o razers2-adeno-hamming-08.sam adeno-genome.fa reads.fasta
20${RAZERS} -vv -of 4 -ds -i 92 -id -o razers2-adeno-edit-08.sam    adeno-genome.fa reads.fasta
21
22${RAZERS} -vv -of 4 -ds -i 96     -o razers2-adeno-hamming-04.sam adeno-genome.fa reads.fasta
23${RAZERS} -vv -of 4 -ds -i 96 -id -o razers2-adeno-edit-04.sam    adeno-genome.fa reads.fasta
24
25# ============================================================
26# Prepare SAM.
27# ============================================================
28
29${RABEMA_PREPARE} -i gold-adeno-hamming-08.sam -o gold-adeno-hamming-08.by_qname.sam
30samtools view -Sb gold-adeno-hamming-08.by_qname.sam > gold-adeno-hamming-08.by_qname.bam
31samtools sort gold-adeno-hamming-08.by_qname.bam gold-adeno-hamming-08.by_coordinate
32samtools view gold-adeno-hamming-08.by_coordinate.bam > gold-adeno-hamming-08.by_coordinate.sam
33${RABEMA_PREPARE} -i gold-adeno-edit-08.sam > gold-adeno-edit-08.by_qname.sam
34samtools view -Sb gold-adeno-edit-08.by_qname.sam -o gold-adeno-edit-08.by_qname.bam
35samtools sort gold-adeno-edit-08.by_qname.bam gold-adeno-edit-08.by_coordinate
36samtools view gold-adeno-edit-08.by_coordinate.bam > gold-adeno-edit-08.by_coordinate.sam
37
38# ============================================================
39# Build Gold Standard
40# ============================================================
41
42${RABEMA_BUILD} --distance-metric hamming -e 8 -o gold-adeno-hamming-08.gsi --reference adeno-genome.fa --in-bam gold-adeno-hamming-08.by_coordinate.sam > gold-adeno-hamming-08.stdout
43${RABEMA_BUILD} --distance-metric edit    -e 8 -o gold-adeno-edit-08.gsi    --reference adeno-genome.fa --in-bam gold-adeno-edit-08.by_coordinate.sam > gold-adeno-edit-08.stdout
44
45# ============================================================
46# Compare Against Gold Standard
47# ============================================================
48
49${RABEMA_EVALUATE} --distance-metric hamming -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-hamming-08.sam --in-gsi gold-adeno-hamming-08.gsi > razers2-adeno-hamming-08.stdout
50${RABEMA_EVALUATE} --distance-metric hamming -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-hamming-04.sam --in-gsi gold-adeno-hamming-08.gsi > razers2-adeno-hamming-04.stdout
51${RABEMA_EVALUATE} --distance-metric edit    -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-edit-08.sam    --in-gsi gold-adeno-edit-08.gsi > razers2-adeno-edit-08.stdout
52${RABEMA_EVALUATE} --distance-metric edit    -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-edit-04.sam    --in-gsi gold-adeno-edit-08.gsi > razers2-adeno-edit-04.stdout
53