temporarily removing black box test, data too big

Author: hannespetur

CMakeLists.txt

@@ -293,7 +293,7 @@ foreach(TEST IN LISTS WEAVER_TESTS)
 endforeach()
 
 ## Add black box test
-add_test(NAME WeaverBlackBox COMMAND sh -c "./weaver index ${CMAKE_CURRENT_SOURCE_DIR}/test/data/test_human_10k.v2.gfa.gz --threads 4 -k 17 -w 5 --vcf=${CMAKE_CURRENT_SOURCE_DIR}/test/data/truth.vcf.gz --log=${CMAKE_CURRENT_BINARY_DIR}/black_box_index.log --vverbose && ./weaver map ${CMAKE_CURRENT_SOURCE_DIR}/test/data/test_human_10k.v2.gfa.gz ${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read1.fq.gz --fq2=${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read2.fq.gz -H ${CMAKE_CURRENT_SOURCE_DIR}/test/data/extra_header_lines.tsv -k 17 -w 5 --log=${CMAKE_CURRENT_BINARY_DIR}/black_box_map.log --vverbose --rta3-quals --fastq-data-buffer-size=650 --max-open-files=12 -r chr20 > ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam && cat ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam | md5sum > ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam.md5")
+# add_test(NAME WeaverBlackBox COMMAND sh -c "./weaver index ${CMAKE_CURRENT_SOURCE_DIR}/test/data/test_human_10k.v2.gfa.gz --threads 4 -k 17 -w 5 --vcf=${CMAKE_CURRENT_SOURCE_DIR}/test/data/truth.vcf.gz --log=${CMAKE_CURRENT_BINARY_DIR}/black_box_index.log --vverbose && ./weaver map ${CMAKE_CURRENT_SOURCE_DIR}/test/data/test_human_10k.v2.gfa.gz ${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read1.fq.gz --fq2=${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read2.fq.gz -H ${CMAKE_CURRENT_SOURCE_DIR}/test/data/extra_header_lines.tsv -k 17 -w 5 --log=${CMAKE_CURRENT_BINARY_DIR}/black_box_map.log --vverbose --rta3-quals --fastq-data-buffer-size=650 --max-open-files=12 -r chr20 > ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam && cat ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam | md5sum > ${CMAKE_CURRENT_BINARY_DIR}/test/output.sam.md5")
 
 # add_test(NAME WeaverBlackBoxDifferentSoff COMMAND sh -c "./weaver map ${CMAKE_CURRENT_SOURCE_DIR}/test/data/test_b38_chr20.gfa ${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read1.fq.gz --fq2=${CMAKE_CURRENT_SOURCE_DIR}/test/data/small.read2.fq.gz -k 19 -w 5 --log=${CMAKE_CURRENT_BINARY_DIR}/black_box_different_soff.log -R \"@RG\\tID:foo\\tPL:ILLUMINA\\tSM:bar\" --vverbose --fastq-data-buffer-size=650 --max-open-files=12 | samtools markdup -u - - | samtools view --remove-tag ms -b -o ${CMAKE_CURRENT_BINARY_DIR}/test/output_different_soff.bam && samtools index ${CMAKE_CURRENT_BINARY_DIR}/test/output_different_soff.bam")