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#!/bin/bash
set -e
pkg=drop-seq
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
# gunzip -r mm10/*
gunzip -r ref/*
gunzip -r org/broadinstitute/dropseq/annotation/*
gunzip -r org/broadinstitute/dropseq/readtrimming/*
mkdir out
#do_stuff_to_test_package#
echo -e "\e[93m\e[1mTest 1\e[0m"
drop-seq TagBamWithReadSequenceExtended INPUT=org/broadinstitute/dropseq/annotation/test.bam \
OUTPUT=out/TagBamWithReadSequenceExtended-cellular.bam SUMMARY=TagBamWithReadSequenceExtended-cellular.bam_summary.txt BASE_RANGE=1-12 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XC NUM_BASES_BELOW_QUALITY=1
samtools view out/TagBamWithReadSequenceExtended-cellular.bam > out/TagBamWithReadSequenceExtended-cellular.sam
diff out/TagBamWithReadSequenceExtended-cellular.sam ref/TagBamWithReadSequenceExtended-cellular.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
echo -e "\e[93m\e[1mTest 2\e[0m"
drop-seq TagBamWithReadSequenceExtended INPUT=org/broadinstitute/dropseq/annotation/test.bam \
OUTPUT=out/TagBamWithReadSequenceExtended-molecular.bam SUMMARY=TagBamWithReadSequenceExtended-molecular.bam_summary.txt BASE_RANGE=1-12 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XM NUM_BASES_BELOW_QUALITY=1
samtools view out/TagBamWithReadSequenceExtended-molecular.bam > out/TagBamWithReadSequenceExtended-molecular.sam
diff out/TagBamWithReadSequenceExtended-molecular.sam ref/TagBamWithReadSequenceExtended-molecular.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
echo -e "\e[93m\e[1mTest 3\e[0m"
drop-seq FilterBam TAG_REJECT=XQ INPUT=org/broadinstitute/dropseq/readtrimming/N701.subset.tagged_filtered.sam \
OUTPUT=out/FilterBam.bam
samtools view out/FilterBam.bam > out/FilterBam.sam
diff out/FilterBam.sam ref/FilterBam.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
echo -e "\e[93m\e[1mTest 4\e[0m"
drop-seq TrimStartingSequence INPUT=out/FilterBam.bam OUTPUT=out/TrimStartingSequence.bam \
OUTPUT_SUMMARY=out/TrimStartingSequence.summary.txt SEQUENCE=AAGCAGTGGTATCAACGCAGAGTGAATGGG MISMATCHES=0 NUM_BASES=5
samtools view out/TrimStartingSequence.bam > out/TrimStartingSequence.sam
diff out/TrimStartingSequence.sam ref/TrimStartingSequence.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
echo -e "\e[93m\e[1mTest 5\e[0m"
drop-seq PolyATrimmer INPUT=out/TrimStartingSequence.bam OUTPUT=out/PolyATrimmer.bam \
OUTPUT_SUMMARY=out/PolyATrimmer.summary.bam MISMATCHES=0 NUM_BASES=6 USE_NEW_TRIMMER=true
samtools view out/PolyATrimmer.bam > out/PolyATrimmer.sam
diff out/PolyATrimmer.sam ref/PolyATrimmer.sam
echo -e "\e[92m\e[1mPassed\e[0m"
echo
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