bad1c2af619824bbeff311b8f0b97d3dc75f9260
markd
  Thu Dec 21 00:45:15 2023 -0800
Work on being able to run tests in parallel.  Due to timing, it might still have issues

diff --git src/hg/utils/vcfToHgvs/tests/makefile src/hg/utils/vcfToHgvs/tests/makefile
index 9da635a..ae8f8e6 100644
--- src/hg/utils/vcfToHgvs/tests/makefile
+++ src/hg/utils/vcfToHgvs/tests/makefile
@@ -1,62 +1,64 @@
 kentSrc = ../../../..
 include ${kentSrc}/inc/common.mk
 
 vcfToHgvs = ${DESTBINDIR}/vcfToHgvs
 
+.NOTPARALLEL:  # table is used by multiple tests
+
 test:: loadTestSet PersonalisGroundTruth2017_agree PersonalisGroundTruth2017_disagree stopLoss
 	${MAKE} clean
 
 # Stable set of RefSeq transcript tables & files for testing Personalis variants:
 loadTestSet:
 	hgLoadSqlTab test -verbose=0 chromInfo ../../../lib/chromInfo.sql PGTdb/chromInfo.tab
 	hgLoadSqlTab test -verbose=0 chromAlias ../../../lib/chromAlias.sql PGTdb/chromAlias.tab
 	hgLoadGenePred test -genePredExt ncbiRefSeq PGTdb/ncbiRefSeq.gp.gz
 	hgLoadPsl test -verbose=0 -table=ncbiRefSeqPsl PGTdb/ncbiRefSeqPsl.psl.gz
 	zcat PGTdb/ncbiRefSeqCds.tab.gz \
 	| hgLoadSqlTab test -verbose=0 ncbiRefSeqCds ~/kent/src/hg/lib/cdsSpec.sql stdin
 	zcat PGTdb/ncbiRefSeqLink.tab.gz \
 	| hgLoadSqlTab test -verbose=0 ncbiRefSeqLink ~/kent/src/hg/lib/ncbiRefSeqLink.sql stdin
 	zcat PGTdb/ncbiRefSeqPepTable.tab.gz \
 	| hgLoadSqlTab test -verbose=0 ncbiRefSeqPepTable ~/kent/src/hg/lib/pepPred.sql stdin
 	gunzip -c PGTdb/seqNcbiRefSeq.rna.fa.gz > PGTdb/seqNcbiRefSeq.rna.fa
 	hgLoadSeq test -verbose=0 -drop -seqTbl=seqNcbiRefSeq -extFileTbl=extNcbiRefSeq \
 	  `pwd`/PGTdb/seqNcbiRefSeq.rna.fa
 
 
 PersonalisGroundTruth2017_agree: mkdirs
 	${vcfToHgvs} test input/$@.vcf output/$@.tab
 	sed -re 's/:/\t/g' output/$@.tab \
 	| awk -F"\t" '{ $$8 = gensub(/[.].*/, "", "", $$8); \
                         if (index($$4, $$8) == 1 && $$14 != $$5) {print;} }' \
 	  > output/$@_differences.tab
 	diff -u expected/$@.tab output/$@.tab
 	diff -u /dev/null output/$@_differences.tab
 
 PersonalisGroundTruth2017_disagree: mkdirs
 	${vcfToHgvs} test input/$@.vcf output/$@.tab
 	sed -re 's/:/\t/g' output/$@.tab \
 	| awk -F"\t" '{ $$8 = gensub(/[.].*/, "", "", $$8); \
                         if (index($$4, $$8) == 1 && $$14 == $$5) {print;} }' \
 	  > output/$@_matches.tab
 	diff -u expected/$@.tab output/$@.tab
 	diff -u /dev/null output/$@_matches.tab
 
 PersonalisGroundTruth2017_patches: mkdirs
 	${vcfToHgvs} hg38 input/$@.vcf output/$@.tab
 	sed -re 's/:/\t/g' output/$@.tab \
 	| awk -F"\t" '{ $$8 = gensub(/[.].*/, "", "", $$8); \
                         if (index($$4, $$8) == 1 && $$14 != $$5) {print;} }' \
 	  > output/$@_differences.tab
 	diff -u expected/$@.tab output/$@.tab
 	diff -u /dev/null output/$@_differences.tab
 
 stopLoss:
 	${vcfToHgvs} hg38 input/$@.vcf stdout | sort -k1,1 -k2n,2n -k3,3 -k6,6 > output/$@.tab
 	diff -u expected/$@.tab output/$@.tab
 
 clean::
 	rm -rf output
 	rm -f PGTdb/seqNcbiRefSeq.rna.fa seqNcbiRefSeq.tab
 
 mkdirs:
 	@${MKDIR} output