#!/usr/bin/env bash

gemma=../bin/gemma

testCenteredRelatednessMatrixKFullLOCO1() {
    outn=mouse_hs1940_full_LOCO1
    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
           -p ../example/mouse_hs1940.pheno.txt \
           -a ../example/mouse_hs1940.anno.txt \
           -loco 1 -gk -debug -o $outn
    assertEquals 0 $?
    outfn=output/$outn.cXX.txt
    assertEquals "1940" `wc -l < $outfn`
    assertEquals "2246.57" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

testUnivariateLinearMixedModelFullLOCO1() {
    outn=mouse_hs1940_CD8_full_LOCO1_lmm
    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
           -p ../example/mouse_hs1940.pheno.txt \
	   -n 1 \
	   -loco 1 \
           -a ../example/mouse_hs1940.anno.txt \
           -k ./output/mouse_hs1940_full_LOCO1.cXX.txt \
	   -lmm \
	   -debug \
           -o $outn
    assertEquals 0 $?
    grep "total computation time" < output/$outn.log.txt
    assertEquals 0 $?
    outfn=output/$outn.assoc.txt
    assertEquals "951" `wc -l < $outfn`
    assertEquals "267507851.98" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

testCenteredRelatednessMatrixK() {
    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
           -p ../example/mouse_hs1940.pheno.txt \
           -gk -o mouse_hs1940 -debug
    assertEquals 0 $?
    outfn=output/mouse_hs1940.cXX.txt
    assertEquals "1940" `wc -l < $outfn`
    assertEquals "3763600" `wc -w < $outfn`
    assertEquals "0.335" `head -c 5 $outfn`
    assertEquals "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

testUnivariateLinearMixedModel() {
    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
           -p ../example/mouse_hs1940.pheno.txt \
           -n 1 \
           -a ../example/mouse_hs1940.anno.txt \
           -k ./output/mouse_hs1940.cXX.txt \
           -lmm \
           -o mouse_hs1940_CD8_lmm \
           -debug
    assertEquals 0 $?
    grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
    assertEquals 0 $?
    outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
    assertEquals "129228" `wc -w < $outfn`
    assertEquals "4038540440.86" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

testMultivariateLinearMixedModel() {
    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
           -p ../example/mouse_hs1940.pheno.txt \
           -n 1 6 \
           -a ../example/mouse_hs1940.anno.txt \
           -k ./output/mouse_hs1940.cXX.txt \
           -lmm -o mouse_hs1940_CD8MCH_lmm \
           -debug
    assertEquals 0 $?

    outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
    assertEquals "139867" `wc -w < $outfn`
    assertEquals "4029037056.54" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

testPlinkStandardRelatednessMatrixK() {
    testname=testPlinkStandardRelatednessMatrixK
    datadir=../example
    outfn=output/$testname.sXX.txt
    rm -f $outfn
    $gemma -bfile $datadir/HLC \
           -gk 2 -o $testname \
           -debug
    assertEquals 0 $?
    assertEquals "427" `wc -l < $outfn`
    assertEquals "-358.07" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

# Test for https://github.com/genetics-statistics/GEMMA/issues/58
# fixed GSLv2 NaN's that appeared with covariates.
testPlinkMultivariateLinearMixedModel() {
    testname=testPlinkMultivariateLinearMixedModel
    datadir=../example
    $gemma -bfile $datadir/HLC \
           -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
           -lmm 1 \
           -maf 0.1 \
           -c $datadir/HLC_covariates.txt \
           -debug \
           -o $testname
    assertEquals 0 $?
    outfn=output/$testname.assoc.txt
    assertEquals "223243" `wc -l < $outfn`
    assertEquals "89757159113.77" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
}

shunit2=`which shunit2`

if [ -x "$shunit2" ]; then
    echo run system shunit2
    . $shunit2
elif [ -e ../contrib/shunit2-2.0.3/src/shell/shunit2 ]; then
    echo run shunit2 provided in gemma repo
    . ../contrib/shunit2-2.0.3/src/shell/shunit2
else
    echo "Can not find shunit2 - see INSTALL.md"
fi