8fdef9e866ecc228bfe4ea54102d0079818f0366
braney
  Fri Apr 8 14:49:38 2022 -0700
let bedGraphToBigWig use chromAlias.bb as chromSizes file.  Add tests
to both bedGraphToBigWig and bedToBigBed

diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile
index a2b89ab..2384bc4 100644
--- src/utils/bedToBigBed/tests/makefile
+++ src/utils/bedToBigBed/tests/makefile
@@ -1,20 +1,36 @@
 kentSrc = ../../..
 A = bedToBigBed
 include ../../../inc/common.mk
 
-test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep
+test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2
+
+testBadChrom1:  outputDir
+	-${BINDIR}/${A} input/colored.genbank.bed input/human.chrom.sizes.txt output/noFile.chromAlias.bb   -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/testBadChrom1.err
+	diff expected/testBadChrom1.err output/testBadChrom1.err
+
+output/human.chromAlias.bb:  outputDir
+	${BINDIR}/${A} input/human.chromAlias.bed input/human.chrom.sizes.txt output/human.chromAlias.bb   -tab -type=bed3+4 -as=input/chromAliasIndex.as -extraIndex=genbank,ensembl,ncbi,ucsc
+
+testBbSize1: outputDir output/human.chromAlias.bb
+	${BINDIR}/${A} input/colored.genbank.bed output/human.chromAlias.bb output/colored.genbank.bb -sizesIsBb -tab -type=bed12+13 -as=input/bigGenePred.as 
+	bigBedToBed output/colored.genbank.bb output/colored.genbank.bed
+	diff input/colored.genbank.bed output/colored.genbank.bed
+
+testBbSize2: outputDir output/human.chromAlias.bb
+	-${BINDIR}/${A} input/mixed.bed output/human.chromAlias.bb output/noFile.chromAlias.bb -sizesIsBb -tab -type=bed12+13 -as=input/bigGenePred.as 2> output/mixed.err
+	diff expected/mixed.err output/mixed.err
 
 testRgb: outputDir
 	${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed input/chrom.sizes output/itemRgb.bb 2> /dev/null
 	bigBedToBed output/itemRgb.bb output/test_itemRgb.bed
 	diff input/itemRgb.bed output/test_itemRgb.bed
 
 testNotSorted: outputDir
 	-${BINDIR}/${A} -type=bed12 input/notSorted.bed input/notSorted.chrom.sizes /dev/null 2> output/notSorted.err || true
 	diff expected/notSorted.err output/notSorted.err
 
 testMultiInsAtEnd: outputDir
 	${BINDIR}/${A} input/multiInsAtEnd.bed input/chrom.sizes output/multiInsAtEnd.bb 2> /dev/null
 	bigBedToBed output/multiInsAtEnd.bb output/test_multiInsAtEnd.bed
 	diff -w input/multiInsAtEnd.bed output/test_multiInsAtEnd.bed