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Do not require strobealign to be in PATH when running tests #348

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merged 1 commit into from
Sep 28, 2023
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Do not require strobealign to be in PATH when running tests #348

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30 changes: 16 additions & 14 deletions tests/run.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
#!/bin/bash
set -xeuo pipefail

strobealign=build/strobealign

if [[ $OSTYPE = linux-gnu ]]; then
color="--color=always"
else
Expand All @@ -15,55 +17,55 @@ function diff() {
build/test-strobealign

# should fail when unknown command-line option used
if strobealign -G > /dev/null 2> /dev/null; then false; fi
if ${strobealign} -G > /dev/null 2> /dev/null; then false; fi

# should succeed when only printing help
strobealign -h > /dev/null
${strobealign} -h > /dev/null

# Ensure the binary is available
samtools --version > /dev/null

# Single-end SAM
strobealign --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.sam
${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library -v tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.sam
diff tests/phix.se.sam phix.se.sam
rm phix.se.sam

# Single-end SAM, M CIGAR operators
strobealign tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.m.sam
${strobealign} tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > phix.se.m.sam
if samtools view phix.se.m.sam | cut -f6 | grep -q '[X=]'; then false; fi

rm phix.se.m.sam

# Paired-end SAM
strobealign --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | grep -v '^@PG' > phix.pe.sam
${strobealign} --eqx --chunk-size 3 --rg-id 1 --rg SM:sample --rg LB:library tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | grep -v '^@PG' > phix.pe.sam
diff tests/phix.pe.sam phix.pe.sam
rm phix.pe.sam

# Single-end PAF
strobealign -x tests/phix.fasta tests/phix.1.fastq | tail -n 11 > phix.se.paf
${strobealign} -x tests/phix.fasta tests/phix.1.fastq | tail -n 11 > phix.se.paf
diff tests/phix.se.paf phix.se.paf
rm phix.se.paf

# Single-end PAF (stdin input)
cat tests/phix.1.fastq | strobealign -x tests/phix.fasta - | tail -n 11 > phix.se.paf
cat tests/phix.1.fastq | ${strobealign} -x tests/phix.fasta - | tail -n 11 > phix.se.paf
diff tests/phix.se.paf phix.se.paf
rm phix.se.paf

# Paired-end PAF
strobealign -x tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | tail -n 11 > phix.pe.paf
${strobealign} -x tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq | tail -n 11 > phix.pe.paf
diff tests/phix.pe.paf phix.pe.paf
rm phix.pe.paf

# Build a separate index
strobealign -r 150 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > without-sti.sam
strobealign -r 150 -i tests/phix.fasta
strobealign -r 150 --use-index tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-sti.sam
${strobealign} -r 150 tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > without-sti.sam
${strobealign} -r 150 -i tests/phix.fasta
${strobealign} -r 150 --use-index tests/phix.fasta tests/phix.1.fastq | grep -v '^@PG' > with-sti.sam
diff without-sti.sam with-sti.sam
rm without-sti.sam with-sti.sam

# Create index requires -r or reads file
if strobealign --create-index tests/phix.fasta > /dev/null 2> /dev/null; then false; fi
if ${strobealign} --create-index tests/phix.fasta > /dev/null 2> /dev/null; then false; fi

# --details output is proper SAM
strobealign --details tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq 2> /dev/null | samtools view -o /dev/null
strobealign --details tests/phix.fasta tests/phix.1.fastq 2> /dev/null | samtools view -o /dev/null
${strobealign} --details tests/phix.fasta tests/phix.1.fastq tests/phix.2.fastq 2> /dev/null | samtools view -o /dev/null
${strobealign} --details tests/phix.fasta tests/phix.1.fastq 2> /dev/null | samtools view -o /dev/null