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#!/usr/bin/env bash
# Preamble
test_path=$(cd `dirname "${BASH_SOURCE[0]}"` && pwd)
test_data_path="$test_path/"$(basename "${BASH_SOURCE[0]}" | sed -e 's@\.t$@@')
source $test_path/setup.sh
freq_in=$test_data_path/frequent_inputs/in.fastq.gz
freq_in2=$test_data_path/frequent_inputs/in2.fastq.gz
freq_in3=$test_data_path/frequent_inputs/in.fasta
freq_in4=$test_data_path/frequent_inputs/in.fasta.gz
freq_in5=$test_data_path/frequent_inputs/in.fastq
plan 21
ref_map
ok_ 'input gzipped fastq' \
000_ingzfastq \
"ustacks -t gzfastq -f $freq_in -o %out" \
ok_ 'input fastq' \
001_infastq \
"ustacks -t fastq -f $freq_in5 -o %out"
ok_ 'input fasta' \
002_infasta \
"ustacks -t fasta -f $freq_in3 -o %out"
ok_ 'inpus gzipped fasta' \
003_ingzfasta \
"ustacks -t gzfasta -f $freq_in4 -o %out"
ok_ 'set sample ID=1 (AKA MySQL column 2)' \
004_sqlid \
"ustacks -t gzfastq -f $freq_in -o %out -i 1"
ok_ 'specify minimum depth of coverage required to call a stack' \
005_mindepcov \
"ustacks -t gzfastq -f $freq_in -o %out -m 3"
ok_ 'specify maximum distance between stacks' \
006_maxdistbtw \
"ustacks -t gzfastq -f $freq_in -o %out -M 3"
ok_ 'specify max distance to align secondary reads to primary stacks' \
007_maxdist_srps \
"ustacks -t gzfastq -f $freq_in -o %out -N 5"
skip_ 'retain unused reads' \
008_retain \
"ustacks -t gzfastq -f %in -o %out -R"
ok_ 'disable haplotype calling from secondary reads' \
009_hapcall \
"ustacks -t gzfastq -f $freq_in -o %out -H"
ok_ 'remove highly repetative (likely error) reads' \
010_remrep \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out -r"
ok_ 'enable deleveraging algorithm' \
011_deleverage \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out -d" \
zip_test
ok_ 'specify max number of stacks at a de novo locus' \
012_maxlocus \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --max_locus_stacks 4"
ok_ 'specify chi square significance level for calling heteroz/homozygote' \
013_alpha0.1 \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --alpha 0.1"
ok_ 'specify chi square significance level for calling heteroz/homozygote' \
014_alpha0.05 \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --alpha 0.05"
ok_ 'specify chi square significance level for calling heteroz/homozygote' \
015_alpha0.01 \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --alpha 0.01"
ok_ 'specify chi square significance level for calling heteroz/homozygote' \
016_alpha0.001 \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --alpha 0.001"
ok_ 'For bounded model, specify upper bound' \
017_bound_high \
"ustacks -t gzfastq -f $freq_in2 -o %out --model_type bounded --bound_high 0.01"
ok_ 'For bounded model, specify lower bound' \
018_bound_low \
"ustacks -t gzfastq -f $freq_in2 -o %out --model_type bounded --bound_low 0.001"
ok_ 'For bounded model, specify upper and lower bounds' \
019_bounded \
"ustacks -t gzfastq -f $freq_in2 -o %out --model_type bounded --bound_low 0.001 --bound_high 0.01"
ok_ 'For fixed model, specify barcode error frequency rate' \
020_fixed \
"ustacks -t gzfastq -f %in/in.fastq.gz -o %out --model_type fixed --bc_err_freq 0.98"
finish
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