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Fix tests #313

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merged 2 commits into from
Jan 23, 2025
Merged

Fix tests #313

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1f71f33
fix github workflow label
AndreaGuarracino Jan 22, 2025
400eeb3
update test for short reads
AndreaGuarracino Jan 23, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/test_on_push.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Expand Up @@ -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(
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4 changes: 4 additions & 0 deletions test/data/regression/reads.255bps.paf
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Original file line number Diff line number Diff line change
@@ -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
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