ef80854d868978e0da8e60f4ec0aad06b10f8a82
braney
  Thu Sep 28 09:42:31 2023 -0700
allow bedToBigBed to use compressed input

diff --git src/utils/bedToBigBed/tests/makefile src/utils/bedToBigBed/tests/makefile
index 53f450b..e561f36 100644
--- src/utils/bedToBigBed/tests/makefile
+++ src/utils/bedToBigBed/tests/makefile
@@ -1,42 +1,47 @@
 kentSrc = ../../..
 A = bedToBigBed
 include ../../../inc/common.mk
 
-test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 testDevStdin testStdin
+test: testRgb testNotSorted testMultiInsAtEnd itemsRgb tabSep testBadChrom1 testBbSize1 testBbSize2 testDevStdin testStdin testCompress
 
 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 -sizesIsChromAliasBb -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 -sizesIsChromAliasBb -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
 
+testCompress: outputDir
+	${BINDIR}/${A} -type=bed9 -as=input/itemRgb.as input/itemRgb.bed.gz 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
 
 itemsRgb: outputDir
 	${BINDIR}/${A} input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null
 	bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed
 	diff input/reservedBed12.bed output/test_reservedBed12.bed
 	${BINDIR}/${A} -type=bed12 input/reservedBed12.bed input/chrom.sizes output/reservedBed12.bb 2> /dev/null
 	bigBedToBed output/reservedBed12.bb output/test_reservedBed12.bed