diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml index c7f7c0fd..d44cf2b4 100644 --- a/.github/workflows/test_on_push.yml +++ b/.github/workflows/test_on_push.yml @@ -47,7 +47,7 @@ jobs: override: true - name: Install wgatools run: cargo install --git https://github.com/wjwei-handsome/wgatools.git - - name: Install wgatools + - name: Install pafcheck run: cargo install --git https://github.com/ekg/pafcheck.git - name: Run wfmash and generate PAF run: build/bin/wfmash -t 8 -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz > test.paf diff --git a/CMakeLists.txt b/CMakeLists.txt index 6d2b9fe8..056ce5bb 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -268,7 +268,7 @@ add_test( 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 200 -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( diff --git a/test/data/regression/reads.255bps.paf b/test/data/regression/reads.255bps.paf index e69de29b..bd0120c6 100644 --- a/test/data/regression/reads.255bps.paf +++ b/test/data/regression/reads.255bps.paf @@ -0,0 +1,4 @@ +S1_180787!>sample!47551848!47552103!+ 257 0 200 + S1_40628!>sample!91808704!91808959!- 257 27 226 193 200 14 gi:f:0.960199 bi:f:0.960199 md:f:0.975053 cg:Z:1I2=1X1=2X70=1D40=1X8=1X72=1I +S1_417507!>sample!115125650!115125903!+ 257 0 200 - S1_77181!>sample!8805734!8805987!+ 257 39 246 180 207 8 gi:f:0.942408 bi:f:0.825688 md:f:0.963921 cg:Z:2=18D24=1X13=1X7=1X35=2X12=1X33=1X8=1X44=1X1=11I1= +S1_825029!>sample!73338!73592!+ 257 0 257 + S1_73315!>sample!73360!73616!+ 257 0 233 226 257 9 gi:f:0.953586 bi:f:0.875969 md:f:0.950569 cg:Z:22I3=3X37=1X16=1I105=1I29=1I15=1D21=2X +S1_1347694!>sample!97761017!97761271!- 255 0 255 + S1_42484!>sample!97761004!97761259!- 257 13 241 226 255 9 gi:f:0.969957 bi:f:0.879377 md:f:0.95939 cg:Z:1=25I8=1I27=1I14=1I14=1D80=1D82=1I