code clean

fixing functest for collapse. Removed redundant prefix in front of all tests to facilitate running individual tests
ACEnglish · Jan 5, 2025 · 9b7fef0 · 9b7fef0
1 parent a779cab
commit 9b7fef0
Show file tree

Hide file tree

Showing 17 changed files with 166 additions and 164 deletions.
diff --git a/repo_utils/sub_tests/anno.sh b/repo_utils/sub_tests/anno.sh
@@ -5,184 +5,184 @@ VCF=$INDIR/variants/multi.vcf.gz
 REF=$INDIR/references/reference.fa
 
 #                                 hompct
-run test_anno_hompct \
+run anno_hompct \
     $truv anno hompct -i $VCF -o $OD/anno_hompct.vcf
-if [ $test_anno_hompct ]; then
+if [ $anno_hompct ]; then
     assert_exit_code 0
     info_tests hompct $OD/anno_hompct.vcf HOMPCT
 fi
 
 #                                 remap
-run test_anno_remap \
+run anno_remap \
     $truv anno remap -H 10 $VCF -r $REF -o $OD/anno_remap.vcf
-if [ $test_anno_remap ]; then
+if [ $anno_remap ]; then
     assert_exit_code 0
     info_tests remap $OD/anno_remap.vcf REMAP,REMAPHits
 fi
 
 #                                 gcpct
-run test_anno_gcpct \
+run anno_gcpct \
     $truv anno gcpct $VCF -r $REF -o $OD/anno_gcpct.vcf
-if [ $test_anno_gcpct ]; then
+if [ $anno_gcpct ]; then
     assert_exit_code 0
     info_tests gcpct $OD/anno_gcpct.vcf GCPCT
 fi
 
 #                                 gtcnt
-run test_anno_gtcnt \
+run anno_gtcnt \
     $truv anno gtcnt $VCF -o $OD/anno_gtcnt.vcf
-if [ $test_anno_gtcnt ]; then
+if [ $anno_gtcnt ]; then
     assert_exit_code 0
     info_tests gtcnt $OD/anno_gtcnt.vcf GTCNT
 fi
 
 #                                 numneigh
-run test_anno_numneigh \
+run anno_numneigh \
     $truv anno numneigh $VCF -o $OD/anno_numneigh.vcf
-if [ $test_anno_numneigh ]; then
+if [ $anno_numneigh ]; then
     assert_exit_code 0
     info_tests numneigh $OD/anno_numneigh.vcf NumNeighbors,NeighId
 fi
 
 #                                 svinfo
-run test_anno_svinfo \
+run anno_svinfo \
     $truv anno svinfo $VCF -o $OD/anno_svinfo.vcf
-if [ $test_anno_svinfo ]; then
+if [ $anno_svinfo ]; then
     assert_exit_code 0
     info_tests svinfo $OD/anno_svinfo.vcf SVTYPE,SVLEN
 fi
 
 #                                 grm
-run test_anno_grm \
+run anno_grm \
     $truv anno grm -i $INDIR/variants/input2.vcf.gz -r $REF -o $OD/grm.jl -t 2
-if [ $test_anno_grm ]; then
+if [ $anno_grm ]; then
     assert_exit_code 0
-    df_check test_anno_grm $ANSDIR/anno/grm.jl $OD/grm.jl
+    df_check anno_grm $ANSDIR/anno/grm.jl $OD/grm.jl
 fi
 
 #                                 trf
-run test_anno_trf \
+run anno_trf \
     $truv anno trf -i $INDIR/variants/multi.vcf.gz \
                    -r $INDIR/beds/repeats.adotto.bed.gz \
                    -f $INDIR/references/reference.fa \
                    -e $INDIR/external/trf  \
                    -m 5 \
                    -o $OD/trf.vcf
-if [ $test_anno_trf ]; then
+if [ $anno_trf ]; then
     assert_exit_code 0
 fi
 
-run test_anno_trf_reg \
+run anno_trf_reg \
     $truv anno trf -i $INDIR/variants/multi.vcf.gz \
                    -r $INDIR/beds/repeats.adotto.bed.gz \
                    -f $INDIR/references/reference.fa \
                    -e $INDIR/external/trf  \
                    -m 5 -R \
                    -o $OD/trf.reg.vcf
-if [ $test_anno_trf_reg ]; then
+if [ $anno_trf_reg ]; then
     assert_exit_code 0
 fi
 
-run test_anno_badparam \
+run anno_badparam \
     $truv anno trf -i $INDIR/input_null.vcf \
                    -r $INDIR/simplerepeat_null.bed \
                    -f $INDIR/reference.fa \
                    -e $INDIR/external/trf_dne  \
                    -o $OD/trf_null.vcf
-if [ $test_anno_badparam ]; then
+if [ $anno_badparam ]; then
     assert_exit_code 1
 fi
 
 # TRF isn't deterministic for some reason, so it can give a different answer in action?
-# run test_anno_trf_result
+# run anno_trf_result
 # assert_equal $(fn_md5 $ANSDIR/trf.vcf) $(fn_md5 $OD/trf.vcf)
 
 #                                 repmask
-run test_anno_repmask \
+run anno_repmask \
     $truv anno repmask -i $INDIR/variants/multi.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py
-if [ $test_anno_repmask ]; then
+if [ $anno_repmask ]; then
     assert_exit_code 0
     assert_equal $(fn_md5 $ANSDIR/anno/repmask.vcf) $(fn_md5 $OD/repmask.vcf)
 fi
 
-run test_anno_repmask_err \
+run anno_repmask_err \
     $truv anno repmask -i $INDIR/variants/input1.vcf.gz -o $OD/repmask.vcf -e $INDIR/external/fakeRM.py
-if [ $test_anno_repmask_err ]; then
+if [ $anno_repmask_err ]; then
     assert_exit_code 1
 fi
 
 #                                 bpovl
-run test_anno_bpovl \
+run anno_bpovl \
     $truv anno bpovl $INDIR/variants/input1.vcf.gz \
                      -o $OD/anno_bpovl.jl \
                      -a $INDIR/misc/anno.gtf.gz -p gff --sizemin 2
-if [ $test_anno_bpovl ]; then
+if [ $anno_bpovl ]; then
     assert_exit_code 0
-    df_check test_anno_bpovl $ANSDIR/anno/anno_bpovl.jl $OD/anno_bpovl.jl
+    df_check anno_bpovl $ANSDIR/anno/anno_bpovl.jl $OD/anno_bpovl.jl
 fi
 
 #                                 density
-run test_anno_density \
+run anno_density \
     $truv anno density $INDIR/variants/input3.vcf.gz \
                        -o $OD/anno_density.jl \
                        -g $INDIR/beds/genome.bed -m $INDIR/beds/mask.bed
-if [ $test_anno_density ]; then
+if [ $anno_density ]; then
     assert_exit_code 0
-    df_check test_anno_density $ANSDIR/anno/anno_density.jl $OD/anno_density.jl
+    df_check anno_density $ANSDIR/anno/anno_density.jl $OD/anno_density.jl
 fi
 
 #                                 dpcnt
-run test_anno_dpcnt \
+run anno_dpcnt \
     $truv anno dpcnt $VCF -o $OD/anno_dpcnt.vcf
-if [ $test_anno_dpcnt ]; then
+if [ $anno_dpcnt ]; then
     assert_exit_code 0
     info_tests dpcnt $OD/anno_dpcnt.vcf DPCNT,ADCNT
 fi
 
 #                                 lcr
-run test_anno_lcr \
+run anno_lcr \
     $truv anno lcr $VCF -o $OD/anno_lcr.vcf
-if [ $test_anno_lcr ]; then
+if [ $anno_lcr ]; then
     assert_exit_code 0
     info_tests lcr $OD/anno_lcr.vcf LCR
 fi
 
 #                                 grpaf
-run test_anno_grpaf \
+run anno_grpaf \
     $truv anno grpaf $INDIR/variants/grpaf.vcf.gz -l $INDIR/misc/grpaf.labels.txt -o $OD/anno_grpaf.vcf
-if [ $test_anno_grpaf ]; then
+if [ $anno_grpaf ]; then
     assert_exit_code 0
     assert_equal $(fn_md5 $ANSDIR/anno/anno_grpaf.vcf) $(fn_md5 $OD/anno_grpaf.vcf)
 fi
 
-run test_anno_grpaf_strict \
+run anno_grpaf_strict \
     $truv anno grpaf --strict $INDIR/variants/grpaf.vcf.gz -l $INDIR/misc/grpaf.labels.txt -o $OD/anno_grpaf.vcf
-if [ $test_anno_grpaf_strict ]; then
+if [ $anno_grpaf_strict ]; then
     assert_exit_code 1
 fi
 
-run test_anno_grpaf_subset \
+run anno_grpaf_subset \
     $truv anno grpaf --tags AF,HWE,ExcHet \
                      $INDIR/variants/grpaf.vcf.gz \
                      -l $INDIR/misc/grpaf.labels.txt \
                      -o $OD/anno_grpaf.subtags.vcf
-if [ $test_anno_grpaf_subset ]; then
+if [ $anno_grpaf_subset ]; then
     assert_exit_code 0
     assert_equal $(fn_md5 $ANSDIR/anno/anno_grpaf.subtags.vcf) $(fn_md5 $OD/anno_grpaf.subtags.vcf)
 fi
 
 #                           add id 
-run test_anno_addid \
+run anno_addid \
     $truv anno addid $INDIR/variants/multi.vcf.gz -o $OD/addid.vcf
-if [ $test_anno_addid ]; then
+if [ $anno_addid ]; then
     assert_exit_code 0
     assert_equal $(fn_md5 $ANSDIR/anno/addid.vcf) $(fn_md5 $OD/addid.vcf)
 fi
 
 
 #                           chunks
-run test_anno_chunks $truv anno chunks $INDIR/variants/multi.vcf.gz -o $OD/chunks.bed
-if [ $test_anno_chunks ]; then
+run anno_chunks $truv anno chunks $INDIR/variants/multi.vcf.gz -o $OD/chunks.bed
+if [ $anno_chunks ]; then
     assert_exit_code 0
     assert_equal $(fn_md5 $ANSDIR/anno/chunks.bed) $(fn_md5 $OD/chunks.bed)
 fi
diff --git a/repo_utils/sub_tests/bench.sh b/repo_utils/sub_tests/bench.sh
@@ -25,71 +25,71 @@ bench_assert() {
     done
 }
 
-run test_bench_12 bench 1 2 12
-if [ $test_bench_12 ]; then
+run bench_12 bench 1 2 12
+if [ $bench_12 ]; then
     bench_assert  12
 fi
 
-run test_bench_13 bench 1 3 13
-if [ $test_bench_13 ]; then
+run bench_13 bench 1 3 13
+if [ $bench_13 ]; then
     bench_assert 13
 fi
 
-run test_bench_23 bench 2 3 23 "--pick multi"
-if [ $test_bench_23 ]; then
+run bench_23 bench 2 3 23 "--pick multi"
+if [ $bench_23 ]; then
     bench_assert 23
 fi
 
 # Testing --includebed
-run test_bench_13_includebed bench 1 3 13_includebed "--includebed $INDIR/beds/include.bed"
-if [ $test_bench_13_includebed ]; then
+run bench_13_includebed bench 1 3 13_includebed "--includebed $INDIR/beds/include.bed"
+if [ $bench_13_includebed ]; then
     bench_assert 13_includebed
 fi
 
 # Testing --extend
-run test_bench_13_extend bench 1 3 13_extend "--includebed $INDIR/beds/include.bed --extend 500"
-if [ $test_bench_13_extend ]; then
+run bench_13_extend bench 1 3 13_extend "--includebed $INDIR/beds/include.bed --extend 500"
+if [ $bench_13_extend ]; then
     bench_assert 13_extend
 fi
 
 
 # --unroll
-run test_bench_unroll $truv bench -b $INDIR/variants/real_small_base.vcf.gz \
+run bench_unroll $truv bench -b $INDIR/variants/real_small_base.vcf.gz \
                                   -c $INDIR/variants/real_small_comp.vcf.gz \
                                   -o $OD/bench_unroll/
-if [ $test_bench_unroll ]; then
+if [ $bench_unroll ]; then
     bench_assert _unroll
 fi
 
 # --pick allele count
-run test_bench_12_gtcomp bench 1 2 12_gtcomp "--pick ac"
-if [ $test_bench_12_gtcomp ]; then
+run bench_12_gtcomp bench 1 2 12_gtcomp "--pick ac"
+if [ $bench_12_gtcomp ]; then
     bench_assert 12_gtcomp
 fi
 
 # --gtcomp edgecase
-run test_bench_gtcomp_edgecase1 $truv bench -b $INDIR/variants/gtcomp_problem1_base.vcf.gz \
+run bench_gtcomp_edgecase1 $truv bench -b $INDIR/variants/gtcomp_problem1_base.vcf.gz \
                                             -c $INDIR/variants/gtcomp_problem1_comp.vcf.gz \
                                             --pick ac \
                                             -o $OD/bench_gtcomp_edgecase1/
-if [ $test_bench_gtcomp_edgecase1 ]; then
+if [ $bench_gtcomp_edgecase1 ]; then
     bench_assert _gtcomp_edgecase1
 fi
-run test_bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD
-if [ $test_bench_badparams ]; then
+run bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD
+if [ $bench_badparams ]; then
     assert_exit_code 100
 fi
 
-run test_bench_starallele $truv bench -b $INDIR/variants/star.base.vcf.gz \
+run bench_starallele $truv bench -b $INDIR/variants/star.base.vcf.gz \
                                       -c $INDIR/variants/star.comp.vcf.gz \
                                       -s 0 -o $OD/bench_starallele/
-if [ $test_bench_starallele ]; then
+if [ $bench_starallele ]; then
     bench_assert _starallele
 fi
 
-run test_bench_bnd $truv bench -b $INDIR/variants/bnd.base.vcf.gz \
+run bench_bnd $truv bench -b $INDIR/variants/bnd.base.vcf.gz \
                                -c $INDIR/variants/bnd.comp.vcf.gz \
                                -p 0 -o $OD/bench_bnd/
-if [ $test_bench_bnd ]; then
+if [ $bench_bnd ]; then
     bench_assert _bnd
 fi