b31907d700c1fe956e4e4c20e64d91de027d7c84
markd
  Tue May 14 02:03:33 2024 -0700
merge blatHuge implementation

diff --git src/blat/test/makefile src/blat/test/makefile
index 46df04b..91d724c 100644
--- src/blat/test/makefile
+++ src/blat/test/makefile
@@ -1,22 +1,76 @@
-all:  tThrowback tIntronMax
+kentSrc = ../..
+include ${kentSrc}/inc/common.mk
+
+blatHuge = ${DESTBINDIR}/blatHuge
+blat = ${DESTBINDIR}/blat
+
+ifeq (${IDXSIZE},64)
+testblat = ${blatHuge}
+else
+testblat = ${blat}
+endif
+
+test::
+	${MAKE} test_idxsize
+	${MAKE} test_idxsize IDXSIZE=64
+	@echo "Note: to run tests on a 40 gbase genome run: make hugeTests" 
+
+test_idxsize: tBasic tThrowback tIntronMax
+
+tBasic:
+	@mkdir -p output/basic
+	${testblat} -verbose=0 basic/hCrea.geno basic/hCrea.mrna output/basic/testRna.psl
+	diff basic/refRna.psl output/basic/testRna.psl
+	${testblat} -verbose=0 -prot basic/hCrea.pep basic/mCrea.pep output/basic/testProt.psl
+	diff basic/refProt.psl output/basic/testProt.psl
+	${testblat} -verbose=0 -t=dnax -q=prot basic/hCrea.geno basic/mCrea.pep output/basic/testProtX.psl
+	diff basic/refProtX.psl output/basic/testProtX.psl
+	${testblat} -verbose=0 -t=dnax -q=rnax basic/hCrea.geno basic/mCrea.mrna output/basic/testRnaX.psl
+	diff basic/refRnaX.psl output/basic/testRnaX.psl
+	${testblat} -verbose=0 -fine basic/hCrea.geno basic/hCrea.mrna output/basic/testFine.psl
+	diff basic/refFine.psl output/basic/testFine.psl
+
 
 tThrowback:
-	blat -verbose=0 throwback/target1.fa throwback/query1.fa throwback/test.psl
-	pslCheck -verbose=0 throwback/test.psl
-	blat -verbose=0 v29skips/ex1_database.fa v29skips/ex1_query.fa v29skips/ex1.psl
-	diff v29skips/ex1_reference.psl v29skips/ex1.psl
-	blat -verbose=0 v29skips/ex2_database.fa v29skips/ex2_query.fa v29skips/ex2.psl
-	diff v29skips/ex2_reference.psl v29skips/ex2.psl
+	@mkdir -p output/v29skips output/throwback
+	${testblat} -verbose=0 throwback/target1.fa throwback/query1.fa output/throwback/test.psl
+	pslCheck -verbose=0 output/throwback/test.psl
+	diff throwback/test.psl output/throwback/test.psl
+	${testblat} -verbose=0 v29skips/ex1_database.fa v29skips/ex1_query.fa output/v29skips/ex1.psl
+	diff v29skips/ex1.psl output/v29skips/ex1.psl
+	${testblat} -verbose=0 v29skips/ex2_database.fa v29skips/ex2_query.fa output/v29skips/ex2.psl
+	diff v29skips/ex2.psl output/v29skips/ex2.psl
 
 tIntronMax:
-	mkdir -p intron50k/out
-	blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test1.psl -minScore=190
-	diff intron50k/expected/test1.psl intron50k/out/test1.psl
-	blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test2.psl -minScore=190 -maxIntron=40000
-	diff intron50k/expected/test2.psl intron50k/out/test2.psl
-	blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test3.psl -minScore=190 -maxIntron=5000
-	diff intron50k/expected/test3.psl intron50k/out/test3.psl
-	rm -rf intron50k/out
+	mkdir -p output/intron50k
+	${testblat} -verbose=0 intron50k/target.fa intron50k/query.fa output/intron50k/test1.psl -minScore=190
+	diff intron50k/test1.psl output/intron50k/test1.psl
+	${testblat} -verbose=0 intron50k/target.fa intron50k/query.fa output/intron50k/test2.psl -minScore=190 -maxIntron=40000
+	diff intron50k/test2.psl output/intron50k/test2.psl
+	${testblat} -verbose=0 intron50k/target.fa intron50k/query.fa output/intron50k/test3.psl -minScore=190 -maxIntron=5000
+	diff intron50k/test3.psl output/intron50k/test3.psl
+
+huge2bit = /hive/data/genomes/asmHubs/GCF/019/279/795/GCF_019279795.1/GCF_019279795.1.2bit
+hugeInputDir = ../../gfServer/tests/input
+
+hugeTests: tHugeUntrans tHugeTrans tHugeProt
+
+tHugeUntrans:
+	@mkdir -p output/hugeUntrans
+	${blatHuge} -verbose=0 ${huge2bit} ${hugeInputDir}/lungfish.rna.fa output/hugeUntrans/lungfish.rna.psl
+	pslCheck -verbose=0 output/hugeUntrans/lungfish.rna.psl
+	diff hugeUntrans/lungfish.rna.psl output/hugeUntrans/lungfish.rna.psl
+
+tHugeTrans:
+	@mkdir -p output/hugeTrans
+	${blatHuge} -verbose=0 -t=dnax -q=rnax ${huge2bit} ${hugeInputDir}/lungfish.rna.fa output/hugeTrans/lungfish.rna.psl
+	pslCheck -verbose=0 output/hugeTrans/lungfish.rna.psl
+	diff hugeTrans/lungfish.rna.psl output/hugeTrans/lungfish.rna.psl
+
+tHugeProt:
+	@mkdir -p output/hugeProt
+	${blatHuge} -verbose=0 -t=dnax -q=prot ${huge2bit} ${hugeInputDir}/lungfish.prot.fa output/hugeProt/lungfish.prot.psl
+	diff hugeProt/lungfish.prot.psl output/hugeProt/lungfish.prot.psl
 
 clean::
-	@echo nothing to clean in blat/test/
+	rm -rf output