5da4fcae9d1a4302be00521ce479dcf678f6f08c
angie
  Fri Mar 11 15:34:09 2011 -0800
Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.

diff --git src/lib/tests/makefile src/lib/tests/makefile
index 1b61d4d..72262b3 100644
--- src/lib/tests/makefile
+++ src/lib/tests/makefile
@@ -1,23 +1,24 @@
 include ../../inc/common.mk
 
 MYLIBDIR = ../../lib/${MACHTYPE}
 MYLIBS = ${MYLIBDIR}/jkweb.a
 BIN_DIR = bin/${MACHTYPE}
 
 test: errCatchTest htmlPageTest htmlExpandUrlTest pipelineTests dyStringTest \
-    mimeTests base64Tests quotedPTests safeTest hashTest fetchUrlTest gff3Test
+    mimeTests base64Tests quotedPTests safeTest hashTest fetchUrlTest gff3Test \
+    tabixTest vcfTest
 	rm -r output fetchUrlTest
 	@echo tested all
 
 mkdirs:
 	${MKDIR} output ${BIN_DIR}
 
 errCatchTest: errCatchTest.o ${MYLIBS} mkdirs
 	${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} ${L}
 	${STRIP} ${BIN_DIR}/errCatchTest${EXE}
 	${BIN_DIR}/errCatchTest secret > output/errCatch.good
 	diff expected/errCatch.good output/errCatch.good
 	${BIN_DIR}/errCatchTest bad > output/errCatch.bad
 	diff expected/errCatch.bad output/errCatch.bad
 
 htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs
@@ -224,17 +225,52 @@
 	diff expected/$@.out output/$@.out
 gff3SpecialCasesTest: ${gff3Tester} mkdirs
 	${gff3Tester} input/specialCasesTest.gff3 output/$@.out
 	diff expected/$@.out output/$@.out
 gff3ErrorCasesTest: ${gff3Tester} mkdirs
 	if ${gff3Tester} input/errorCasesTest.gff3 /dev/null >output/$@.err 2>&1 ; then exit 0 else exit 1; fi
 	diff expected/$@.err output/$@.err
 gff3DiscontiousTest: ${gff3Tester} mkdirs
 	${gff3Tester} input/discontinuous.gff3 output/$@.out
 	diff expected/$@.out output/$@.out
 
 ${BIN_DIR}/gff3Tester: gff3Tester.o ${MYLIBS}
 	${MKDIR} ${BIN_DIR}
 	${CC} ${COPT} -o ${BIN_DIR}/gff3Tester gff3Tester.o ${MYLIBS} ${L}
 
+
+# lineFile's tabix support:
+tabixTester=${BIN_DIR}/tabixFetch
+tabixTest: tabixFetch1kGNoGenotypes tabixFetch1kGWithGenotypes
+
+tabixFetch1kGNoGenotypes: ${tabixTester} mkdirs
+	${tabixTester} input/YRI.trio.2010_06.novelsequences.sites.vcf.gz 2:26790860-194631353 > output/$@.out
+	diff expected/$@.out output/$@.out
+
+tabixFetch1kGWithGenotypes: ${tabixTester} mkdirs
+	${tabixTester} input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz 2:26793738-26794385 > output/$@.out
+	diff expected/$@.out output/$@.out
+
+${BIN_DIR}/tabixFetch: tabixFetch.o ${MYLIBS}
+	${MKDIR} ${BIN_DIR}
+	${CC} ${COPT} -o ${BIN_DIR}/tabixFetch tabixFetch.o ${MYLIBS} ${L}
+
+
+# vcf:
+vcfTester=${BIN_DIR}/vcfParseTest
+vcfTest: vcfParse1kGNoGenotypes vcfParse1kGWithGenotypes
+
+vcfParse1kGNoGenotypes: ${vcfTester} mkdirs
+	${vcfTester} input/YRI.trio.2010_06.novelsequences.sites.vcf.gz 2 26790859 194631353 > output/$@.out
+	diff expected/$@.out output/$@.out
+
+vcfParse1kGWithGenotypes: ${vcfTester} mkdirs
+	${vcfTester} input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz 2 26793737 26794385 > output/$@.out
+	diff expected/$@.out output/$@.out
+
+${BIN_DIR}/vcfParseTest: vcfParseTest.o ${MYLIBS}
+	${MKDIR} ${BIN_DIR}
+	${CC} ${COPT} -o ${BIN_DIR}/vcfParseTest vcfParseTest.o ${MYLIBS} ${L}
+
+
 clean:
 	rm -rf *.o bin output *.tmp mimeTester.tmp mimeTester.out fetchUrlTest