diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 2dd2437f28091c6ddb32792926c65372388ef085..6798779f957745df6b7e0509e6feb1819a236372 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -3,7 +3,7 @@ default: stages: - buildStatic - + - release variables: before_script: @@ -18,3 +18,13 @@ buildStatic: script: - /usr/local/bin/nsb -s ./src/sscocaller.nim -n sscocaller.nimble -o . -- --d:release --threads:on - ls -l ./src + + + +#release: +#i tag_name: $CI_COMMIT_TAG +# script: +# - echo "create static build" +# image: registry.gitlab.com/gitlab-org/release-cli:latest + + diff --git a/tests/AAAGTAGCACGTCTCT-1.raw.bam b/tests/AAAGTAGCACGTCTCT-1.raw.bam new file mode 100644 index 0000000000000000000000000000000000000000..38a39fc2875c64462541eb9f41c908e50c1621a3 Binary files /dev/null and b/tests/AAAGTAGCACGTCTCT-1.raw.bam differ diff --git a/tests/AAAGTAGCACGTCTCT-1.raw.bam.bai b/tests/AAAGTAGCACGTCTCT-1.raw.bam.bai new file mode 100644 index 0000000000000000000000000000000000000000..c06d0dac0e1777182acb380cf2b6c1862b4b075a Binary files /dev/null and b/tests/AAAGTAGCACGTCTCT-1.raw.bam.bai differ diff --git a/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz b/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..354857abfd1d4ccd2a2db9faf368ac80447a36f7 Binary files /dev/null and b/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz differ diff --git a/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz.csi b/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz.csi new file mode 100644 index 0000000000000000000000000000000000000000..68f8cd4c6f21e670f398e202655660dec88092fa Binary files /dev/null and b/tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz.csi differ diff --git a/tests/bcAA.tsv b/tests/bcAA.tsv new file mode 100644 index 0000000000000000000000000000000000000000..5d5963dd3118872e9fd0e904a2c567c6d2d45eed --- /dev/null +++ b/tests/bcAA.tsv @@ -0,0 +1,2 @@ +AAAGTAGCACGTCTCT-1 +AAAGTAGCACGTCTCT-1 diff --git a/tests/ccsnp-6_altCountEXP.mtx b/tests/ccsnp-6_altCountEXP.mtx new file mode 100644 index 0000000000000000000000000000000000000000..6501d18c1aaea02d23d5a282f4281bb7055d2eef --- /dev/null +++ b/tests/ccsnp-6_altCountEXP.mtx @@ -0,0 +1,4 @@ +%%MatrixMarket matrix coordinate integer general +2 1 2 +1 1 3 +2 1 4 diff --git a/tests/ccsnp-6_totalCountEXP.mtx b/tests/ccsnp-6_totalCountEXP.mtx new file mode 100644 index 0000000000000000000000000000000000000000..8a01fd5e385767b988f0278aee7c548cf14dcd85 --- /dev/null +++ b/tests/ccsnp-6_totalCountEXP.mtx @@ -0,0 +1,4 @@ +%%MatrixMarket matrix coordinate integer general +2 1 2 +1 1 4 +2 1 4 diff --git a/tests/ccsnp-6_viEXP.mtx b/tests/ccsnp-6_viEXP.mtx new file mode 100644 index 0000000000000000000000000000000000000000..3fdc677b62b449b1c19944a6039f4730e4a81e13 --- /dev/null +++ b/tests/ccsnp-6_viEXP.mtx @@ -0,0 +1,4 @@ +%%MatrixMarket matrix coordinate integer general +2 1 2 +2 1 2 +1 1 2 diff --git a/tests/ccsnp-6_viSegInfoEXP.txt b/tests/ccsnp-6_viSegInfoEXP.txt new file mode 100644 index 0000000000000000000000000000000000000000..1676efbb7f347ea3c3d82937f99aae5127072d65 --- /dev/null +++ b/tests/ccsnp-6_viSegInfoEXP.txt @@ -0,0 +1 @@ +ithSperm0 129322470 147594395 13.18334746401731 2 2 diff --git a/tests/test.sh b/tests/test.sh index b4ec888a7b58570bdebfb1c1788bcce346f7ad3e..4d61099fcd9473592604c9ae26dae17ed1490eeb 100644 --- a/tests/test.sh +++ b/tests/test.sh @@ -1,2 +1,28 @@ -./code/sscocaller --threads 2 --chrom 6 data/AAAGTAGCACGTCTCT-1.raw.bam data/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz data/bcAA.tsv ./percell/ccsnp- +#!/bin/bash + + +./src/sscocaller --threads 2 --chrom 6 tests/AAAGTAGCACGTCTCT-1.raw.bam tests/AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz tests/bcAA.tsv ./tests/tests- + +test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest + +chmod 755 ssshtest + +source ./ssshtest + +set -o nounset + +STOP_ON_FAIL=0 + +run test_no_stdout diff tests/ccsnp-6_viSegInfoEXP.txt tests/tests-6_viSegInfo.txt +assert_no_stdout +assert_exit_code $EX_OK + +run test_no_stdout diff tests/ccsnp-6_totalCountEXP.mtx tests/tests-6_totalCount.mtx +assert_no_stdout +assert_exit_code $EX_OK + +run test_no_stdout diff tests/ccsnp-6_totalCountEXP.mtx tests/tests-6_totalCountEXP.mtx +assert_no_stdout +assert_exit_code $EX_ERROR +