This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository bedtools.
commit f62bafa2b4b0b91e39fcec94a0c6c825dc3e0ee2 Author: Charles Plessy <[email protected]> Date: Mon Jan 5 10:30:07 2015 +0900 Conforms to Policy 3.9.6. --- debian/control | 2 +- src/utils/FileRecordTools/FileReaders/Makefile~ | 41 -- test/intersect/new_test-intersect.sh~ | 766 ------------------------ 3 files changed, 1 insertion(+), 808 deletions(-) diff --git a/debian/control b/debian/control index dd86f26..b95c52e 100644 --- a/debian/control +++ b/debian/control @@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 9), python, zlib1g-dev, samtools -Standards-Version: 3.9.5 +Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bedtools.git Vcs-Git: git://anonscm.debian.org/debian-med/bedtools.git Homepage: http://code.google.com/p/bedtools/ diff --git a/src/utils/FileRecordTools/FileReaders/Makefile~ b/src/utils/FileRecordTools/FileReaders/Makefile~ deleted file mode 100644 index 37ff6e8..0000000 --- a/src/utils/FileRecordTools/FileReaders/Makefile~ +++ /dev/null @@ -1,41 +0,0 @@ -OBJ_DIR = ../../../../obj/ -BIN_DIR = ../../../../bin/ -UTILITIES_DIR = ../../../utils/ -# ------------------- -# define our includes -# ------------------- -INCLUDES = -I$(UTILITIES_DIR)/BamTools/include/ \ - -I$(UTILITIES_DIR)/BamTools/src/ \ - -I$(UTILITIES_DIR)/fileType/ \ - -I$(UTILITIES_DIR)/Contexts/ \ - -I$(UTILITIES_DIR)/GenomeFile/ \ - -I$(UTILITIES_DIR)/general/ \ - -I$(UTILITIES_DIR)/gzstream/ \ - -I$(UTILITIES_DIR)/version/ - - -# ---------------------------------- -# define our source and object files -# ---------------------------------- -SOURCES= FileReader.h FileReader.cpp SingleLineDelimTransferBuffer.h SingleLineDelimTransferBuffer.cpp \ - SingleLineDelimTextFileReader.h SingleLineDelimTextFileReader.cpp BamFileReader.h BamFileReader.cpp \ - BufferedStreamMgr.h BufferedStreamMgr.cpp InputStreamMgr.h InputStreamMgr.cpp -OBJECTS= FileReader.o SingleLineDelimTransferBuffer.o SingleLineDelimTextFileReader.o BamFileReader.o BufferedStreamMgr.o InputStreamMgr.o -_EXT_OBJECTS=ParseTools.o QuickString.o CompressionTools.o -EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS)) -BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) - -all: $(BUILT_OBJECTS) - -.PHONY: all - -$(BUILT_OBJECTS): $(SOURCES) - @echo " * compiling" $(*F).cpp - @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) - -clean: - @echo "Cleaning up." - @rm -f $(OBJ_DIR)/FileReader.o $(OBJ_DIR)SingleLineDelimTransferBuffer $(OBJ_DIR)/SingleLineDelimTextFileReader.o \ - $(OBJ_DIR)/BinaryFileReader.o $(OBJ_DIR)/BamFileReader.o $(OBJ_DIR)/BufferedStreamMgr.o $(OBJ_DIR)/InputStreamMgr.o $(OBJ_DIR)/PushBackGzStream.o - -.PHONY: clean diff --git a/test/intersect/new_test-intersect.sh~ b/test/intersect/new_test-intersect.sh~ deleted file mode 100755 index 55b01ed..0000000 --- a/test/intersect/new_test-intersect.sh~ +++ /dev/null @@ -1,766 +0,0 @@ -BT=${BT-../../bin/bedtools} - -check() -{ - if diff $1 $2; then - echo ok - else - echo fail - fi -} - -########################################################### -# Test intersection of a as bed from file vs b as bed from file -############################################################ -echo " intersect.new.t01...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a.bed -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bed from redirect vs b as bed from file -############################################################ -echo " intersect.new.t02...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bed from pipe vs b as bed from file -############################################################ -echo " intersect.new.t03...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a.bed | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bed from fifo vs b as bed from file -############################################################ -echo " intersect.new.t04...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a.bed) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as gzipped from file vs b as bed from file -############################################################ -echo " intersect.new.t05...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a_gzipped.bed.gz -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as gzipped from redirect vs b as bed from file -############################################################ -echo " intersect.new.t06...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a_gzipped.bed.gz > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as gzipped from pipe vs b as bed from file -############################################################ -echo " intersect.new.t07...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a_gzipped.bed.gz | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as gzipped from fifo vs b as bed from file -############################################################ -echo " intersect.new.t08...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a_gzipped.bed.gz) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bgzipped from file vs b as bed from file -############################################################ -echo " intersect.new.t09...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a_bgzipped.bed.gz -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bgzipped from redirect vs b as bed from file -############################################################ -echo " intersect.new.t10...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a_bgzipped.bed.gz > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bgzipped from pipe vs b as bed from file -############################################################ -echo " intersect.new.t11...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a_bgzipped.bed.gz | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bgzipped from fifo vs b as bed from file -############################################################ -echo " intersect.new.t12...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a_bgzipped.bed.gz) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a as bam from file vs b as bed from file -############################################################ -echo " intersect.new.t13...\c" -$BT intersect -a a.bam -b b.bed> obs -check obs aVSb.bam -rm obs - - -########################################################### -# Test intersection of a as bam from redirect vs b as bed from file -############################################################ -echo " intersect.new.t14...\c" -$BT intersect -a - -b b.bed < a.bam> obs -check obs aVSb.bam -rm obs - - -########################################################### -# Test intersection of a as bam from pipe vs b as bed from file -############################################################ -echo " intersect.new.t15...\c" -cat a.bam | $BT intersect -a - -b b.bed> obs -check obs aVSb.bam -rm obs - - -########################################################### -# Test intersection of a as bam from fifo vs b as bed from file -############################################################ -echo " intersect.new.t16...\c" -$BT intersect -a <(cat a.bam) -b b.bed > obs -check obs aVSb.bam -rm obs - - -########################################################### -# Test intersection of bam file containing both good reads -# and those where both read and mate are unmapped vs b file -# as bed. -############################################################ -echo " intersect.new.t17...\c" -echo \ -"chr1 100 101 a2 255 - 100 200 0,0,0 1 100, 0, -chr1 100 110 a2 255 - 100 200 0,0,0 1 100, 0," > exp -$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of bam file containing both good reads -# and those where both read and mate are unmapped vs b file -# as bed, with noHit (-v) option. -############################################################ -echo " intersect.new.t18...\c" -echo \ -"chr1 10 20 a1 255 + 10 20 0,0,0 1 10, 0, -. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/1 0 . -1 -1 -1 0,0,0 0 . . -. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/2 0 . -1 -1 -1 0,0,0 0 . . -. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/1 0 . -1 -1 -1 0,0,0 0 . . -. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/2 0 . -1 -1 -1 0,0,0 0 . . -. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/1 0 . -1 -1 -1 0,0,0 0 . . -. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/2 0 . -1 -1 -1 0,0,0 0 . ." > exp -$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed -v > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of bam file containing read where query -# is mapped and mate is not. -############################################################ -echo " intersect.new.t19...\c" -echo \ -"chr1 98650 98704 FCC1MK2ACXX:1:1212:13841:9775#/1 0 + 98604 98704 0,0,0 1 100, 0," > exp -$BT intersect -a oneUnmapped.bam -b j1.bed -bed > obs -check obs exp -rm obs exp - -########################################################### -# Test intersection of bam file containing read where query -# is mapped and mate is not, with noHit (-v) option. -############################################################ -echo " intersect.new.t20...\c" -echo \ -"chr1 -1 -1 FCC1MK2ACXX:1:1212:13841:9775#/2 0 . -1 -1 -1 0,0,0 0 . ." > exp -$BT intersect -a oneUnmapped.bam -b j1.bed -bed -v > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of bam file containing read where query -# is unmapped but mate is mapped. -############################################################ -echo " intersect.new.t20.b...\c" -touch exp -$BT intersect -a queryUnmappedMateMappedCoordsInvalid.bam -b j1.bed -bed > obs -check obs exp -rm obs exp - -########################################################### -# Test intersection of bam file containing read where one -# mate is mapped and one is not, with noHit (-v) option. -############################################################ -echo " intersect.new.t20.c...\c" -echo ". -1 -1 TTTACCTTT:4FSQ5P1:286:D2GA7ACXX:6:2316:20858:89646 0 . -1 -1 -1 0,0,0 0 . ." > exp -$BT intersect -a queryUnmappedMateMappedCoordsInvalid.bam -b j1.bed -bed -v > obs -check obs exp -rm obs exp - - - - - -########################################################### -# Test intersection with -sorted, see that order specified -# in genome file is enforced. -############################################################ -echo " intersect.new.t21...\c" -echo \ -"Error: Sorted input specified, but the file chromOrderA.bed has the following record with a different sort order than the genomeFile human.hg19.genome -chr10 10 20 a3 100 +" > exp -$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted -g human.hg19.genome 2>obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection with -sorted, see that hits are missed -# With no genome file -############################################################ -echo " intersect.new.t22...\c" -echo \ -"chr1 15 20 a1 100 + -chr2 15 20 a2 100 + -chrX 15 20 a5 100 +" > exp -$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection with -sorted, see that hits are correct -# when sort order of files matches genome file sort order -############################################################ -echo " intersect.new.t23...\c" -echo \ -"chr1 15 20 a1 100 + -chr2 15 20 a2 100 + -chr10 15 20 a3 100 + -chr11 15 20 a4 100 + -chrX 15 20 a5 100 + -chrM 15 20 a6 100 +" > exp -$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted -g human.hg19.vSort.genome > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bed from file vs b as bed from file -############################################################ -echo " intersect.new.t24...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a_withLargeHeader.bed -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bed from redirect vs b as bed from file -############################################################ -echo " intersect.new.t25...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a_withLargeHeader.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bed from pipe vs b as bed from file -############################################################ -echo " intersect.new.t26...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a_withLargeHeader.bed | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bed from fifo vs b as bed from file -############################################################ -echo " intersect.new.t27...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a_withLargeHeader.bed) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as gzipped from file vs b as bed from file -############################################################ -echo " intersect.new.t28...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a_withLargeHeader_gzipped.bed.gz -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as gzipped from redirect vs b as bed from file -############################################################ -echo " intersect.new.t29...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a_withLargeHeader_gzipped.bed.gz > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as gzipped from pipe vs b as bed from file -############################################################ -echo " intersect.new.t30...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a_withLargeHeader_gzipped.bed.gz | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as gzipped from fifo vs b as bed from file -############################################################ -echo " intersect.new.t31...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a_withLargeHeader_gzipped.bed.gz) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bgzipped from file vs b as bed from file -############################################################ -echo " intersect.new.t32...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a a_withLargeHeader_bgzipped.bed.gz -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bgzipped from redirect vs b as bed from file -############################################################ -echo " intersect.new.t33...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a - -b b.bed < a_withLargeHeader_bgzipped.bed.gz > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bgzipped from pipe vs b as bed from file -############################################################ -echo " intersect.new.t34...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -cat a_withLargeHeader_bgzipped.bed.gz | $BT intersect -a - -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bgzipped from fifo vs b as bed from file -############################################################ -echo " intersect.new.t35...\c" -echo \ -"chr1 100 101 a2 2 - -chr1 100 110 a2 2 -" > exp -$BT intersect -a <(cat a_withLargeHeader_bgzipped.bed.gz) -b b.bed > obs -check obs exp -rm obs exp - - -########################################################### -# Test intersection of a with large header as bed from file -# vs b as bed from file, and print header -############################################################ -echo " intersect.new.t36...\c" -$BT intersect -a a_withLargeHeader.bed -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bed from -# redirect vs b as bed from file, and print header -############################################################ -echo " intersect.new.t37...\c" -$BT intersect -a - -b b.bed < a_withLargeHeader.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bed from pipe -# vs b as bed from file, and print header -############################################################ -echo " intersect.new.t38...\c" -cat a_withLargeHeader.bed | $BT intersect -a - -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bed from fifo -# vs b as bed from file, and print header -############################################################ -echo " intersect.new.t39...\c" -$BT intersect -a <(cat a_withLargeHeader.bed) -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as gzipped from -# file vs b as bed from file, and print header -############################################################ -echo " intersect.new.t40...\c" -$BT intersect -a a_withLargeHeader_gzipped.bed.gz -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as gzipped from -# redirect vs b as bed from file, and print header -############################################################ -echo " intersect.new.t41...\c" -$BT intersect -a - -b b.bed < a_withLargeHeader_gzipped.bed.gz -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as gzipped from -# pipe vs b as bed from file, and print header -############################################################ -echo " intersect.new.t42...\c" -cat a_withLargeHeader_gzipped.bed.gz | $BT intersect -a - -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as gzipped from -# fifo vs b as bed from file, and print header -############################################################ -echo " intersect.new.t43...\c" -$BT intersect -a <(cat a_withLargeHeader_gzipped.bed.gz) -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bgzipped from -# file vs b as bed from file, and print header -############################################################ -echo " intersect.new.t44...\c" -$BT intersect -a a_withLargeHeader_bgzipped.bed.gz -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bgzipped from -# redirect vs b as bed from file, and print header -############################################################ -echo " intersect.new.t45...\c" -$BT intersect -a - -b b.bed < a_withLargeHeader_bgzipped.bed.gz -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bgzipped from -# pipe vs b as bed from file, and print header -############################################################ -echo " intersect.new.t46...\c" -cat a_withLargeHeader_bgzipped.bed.gz | $BT intersect -a - -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test intersection of a with large header as bgzipped from -# fifo vs b as bed from file, and print header -############################################################ -echo " intersect.new.t47...\c" -$BT intersect -a <(cat a_withLargeHeader_bgzipped.bed.gz) -b b.bed -header > obs -check obs aWithHeaderVsB.txt -rm obs - - -########################################################### -# Test enforcement of sort order when using -sorted option. -# Show that detect chrom "jumping", i.e. chr1, chr2, then -# back to chr1 -############################################################ -echo " intersect.new.t48...\c" -echo "Error: Sorted input specified" > exp -$BT intersect -a chromsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 -d ',' > obs -check obs exp -rm obs exp - -########################################################### -# Test enforcement of sort order when using -sorted option. -# Show that detect chrom "jumping", i.e. chr1, chr2, then -# back to chr1 -############################################################ -echo " intersect.new.t49...\c" -echo "Error: Sorted input specified" > exp -$BT intersect -a recordsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 -d ',' > obs -check obs exp -rm obs exp - -########################################################### -# Test that we throw an error for non-existant files -############################################################ -echo " intersect.new.t50...\c" -echo "Error: Unable to open file nonExistantFile.bed. Exiting." > exp -$BT intersect -a nonExistantFile.bed -b b.bed -sorted 2>&1 > /dev/null | cat - >obs -check obs exp -rm obs exp - -########################################################### -# Test that we allow empty query files -############################################################ -echo " intersect.new.t51...\c" -touch exp -touch dummy.txt -$BT intersect -a dummy.txt -b b.bed 2>&1 > /dev/null | cat - > obs -check obs exp -rm obs exp dummy.txt - - -########################################################### -# Test that we throw an error for unrecognized arguments -############################################################ -echo " intersect.new.t52...\c" -echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp -$BT intersect -a a.bed -b b.bed -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs -check obs exp -rm obs exp - - -########################################################### -# Test that we can process a Bam file with no text in -# it's header. -############################################################ -echo " intersect.new.t53...\c" -$BT intersect -a gdc.bam -b gdc.bam -bed > obs -check obs gdc_exp -rm obs - -########################################################### -# Test that if the query is BAM, and bed output is not -# explicit, and they asked for an output option that is not -# valid with BAM output, an error is thrown. -############################################################ -echo " intersect.new.t54...\c" -echo "***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****" > exp -$BT intersect -a a.bam -b b.bed -wao 2>&1 > /dev/null | head -2 | tail -1 > obs -check obs exp -rm obs exp - - -########################################################### -# Test that gff files work correctly -############################################################ -echo " intersect.new.t55...\c" -echo \ -"chr2L . UTR 50 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2; -chr2L . CDS 71 100 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2; -chr2L . exon 50 100 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2; -chr2L . mRNA 50 100 0 + . ID=mRNA:xs2;Parent=g2; -chr2L . gene 50 100 0 + . ID=g2;" > exp -$BT intersect -a gdc.gff -b gdc_one.bed > obs -check obs exp -rm obs exp - -########################################################### -# Test that we allow empty database files, unsorted -############################################################ -echo " intersect.new.t56...\c" -touch exp -touch dummy.txt -$BT intersect -a a.bed -b dummy.txt 2>&1 > /dev/null | cat - > obs -check obs exp -rm obs exp dummy.txt - -########################################################### -# Test that we allow empty database files, sorted -############################################################ -echo " intersect.new.t57...\c" -touch exp -touch dummy.txt -$BT intersect -a a.bed -b dummy.txt -sorted 2>&1 > /dev/null | cat - > obs -check obs exp -rm obs exp dummy.txt - - -########################################################### -# Test that we allow empty database files, unsorted, with -# -v (noHit) option -############################################################ -echo " intersect.new.t58...\c" -touch dummy.txt -$BT intersect -a a.bed -b dummy.txt -v > obs -check obs a.bed -rm obs dummy.txt - - -########################################################### -# Test that an empty query with header run with -header -# option will print header -############################################################ -echo " intersect.new.t59...\c" -echo "#Random Header" >dummy.txt -$BT intersect -a dummy.txt -b a.bed -header > obs -check obs dummy.txt -rm obs dummy.txt - - -########################################################### -# Test that an empty query with header, gzipped, that -# runs with -header option will print header -############################################################ -echo " intersect.new.t60...\c" -echo "#Random Header" >dummy.txt -gzip dummy.txt -echo "#Random Header" >exp -$BT intersect -a dummy.txt.gz -b a.bed -header > obs -check obs exp -rm obs dummy.txt.gz exp - -########################################################### -# Test that an empty query with header, bgzipped, that -# runs with -header option will print header -############################################################ -echo " intersect.new.t61...\c" -echo "#Random Header" >dummy.txt -bgzip dummy.txt -echo "#Random Header" >exp -$BT intersect -a dummy.txt.gz -b a.bed -header > obs -check obs exp -rm obs dummy.txt.gz exp - - -########################################################### -# Test that an empty VCF query with header that -# runs with -header option will print header -############################################################ -echo " intersect.new.t62...\c" -$BT intersect -a headerOnly.vcf -b a.bed -header > obs -check obs headerOnly.vcf -rm obs - - -########################################################### -# Test that files with DOS newline characters, '\r', -# and/or extra tabs at end of line are handled -############################################################ -echo " intersect.new.t63...\c" -echo \ -"chr1 11323785 11617177 -chr1 12645605 13926923 -chr1 14750216 15119039" >exp -~/mergeBugSpace/bt2-merge-debug/bin/bedtools intersect -a dosLineChar_a.bed -b dosLineCharWithExtraTab_b.bed -v > obs -check exp obs -rm exp obs - -########################################################### -# Test that files with no newlines at all are handled -############################################################ -echo " intersect.new.t64...\c" -echo "chr17 7577068 7577157" > exp -$BT intersect -a oneRecordNoNewline.bed -b oneRecordNoNewline.bed > obs -check obs exp -rm obs exp - -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
