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Revert on disabling tests and adding updated regression output #309

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merged 3 commits into from
Jan 22, 2025
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Revert on disabling tests and adding updated regression output #309

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92e1f95
Revert "update test"
pjotrp Jan 22, 2025
9b7a6f2
Modified test output after reverting Andreas patch that disabled thes…
pjotrp Jan 22, 2025
c9b3855
Merge branch 'revert-test'
pjotrp Jan 22, 2025
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12 changes: 7 additions & 5 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -258,29 +258,31 @@ add_test(

add_test(
NAME wfmash-mapping-coverage-with-8-yeast-genomes-to-PAF
COMMAND bash -c "${INVOKE} data/scerevisiae8.fa.gz -p 95 -n 7 -m -L -Y \\# > scerevisiae8.paf && ./scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 && head -3000 scerevisiae8.paf > scerevisiae8.paf.output"
COMMAND bash -c "${INVOKE} data/scerevisiae8.fa.gz -p 95 -n 7 -m -L -Y \\# > scerevisiae8.paf && ./scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 && head -3000 scerevisiae8.paf > scerevisiae8.paf.output && ${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/scerevisiae8.paf.output scerevisiae8.paf.output"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

add_test(
NAME wfmash-short-reads-500bps-to-SAM
COMMAND bash -c "${INVOKE} data/reference.fa.gz data/reads.500bps.fa.gz -s 0.5k -N -a > reads.500bps.sam && samtools view reads.500bps.sam -bS | samtools sort > reads.500bps.bam && samtools index reads.500bps.bam && samtools view reads.500bps.bam | head > wfmash-short-reads-500bps-to-SAM.output"
COMMAND bash -c "${INVOKE} data/reference.fa.gz data/reads.500bps.fa.gz -s 0.5k -N -a > reads.500bps.sam && samtools view reads.500bps.sam -bS | samtools sort > reads.500bps.bam && samtools index reads.500bps.bam && samtools view reads.500bps.bam | head > wfmash-short-reads-500bps-to-SAM.output && ${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/wfmash-short-reads-500bps-to-SAM.output wfmash-short-reads-500bps-to-SAM.output"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

add_test(
NAME wfmash-short-reads-255bps-to-PAF
COMMAND bash -c "${INVOKE} data/reads.255bps.fa.gz -w 16 -s 100 -L > reads.255bps.paf && head reads.255bps.paf" # && ${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/reads.255bps.paf reads.255bps.paf"
COMMAND bash -c "${INVOKE} data/reads.255bps.fa.gz -w 16 -s 100 -L > reads.255bps.paf && head reads.255bps.paf && ${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/reads.255bps.paf reads.255bps.paf"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

add_test(
NAME wfmash-input-mapping
COMMAND bash -c "${INVOKE} data/scerevisiae8.fa.gz -p 95 -T S288C -Q SK1 -m > mappings.paf && \
${INVOKE} data/scerevisiae8.fa.gz -i mappings.paf|sort > aligned.paf.output"
${INVOKE} data/scerevisiae8.fa.gz -i mappings.paf|sort > aligned.paf.output && \
${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/aligned.paf.output aligned.paf.output"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

add_test(
NAME wfmash-all2all
COMMAND bash -c "${INVOKE} -t 8 data/scerevisiae8.fa.gz > all2all.paf && \
sort all2all.paf | head -300 > all2all-300.paf.output"
sort all2all.paf | head -300 > all2all-300.paf.output && \
${CMAKE_COMMAND} -E compare_files ${REGRESSION_TEST_DIR}/all2all-300.paf.output all2all-300.paf.output"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

install(TARGETS wfmash DESTINATION bin)
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