Merge pull request #313 from waveygang/fix_tests

Fix tests

.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

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(

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