[med-svn] [bedtools] 03/04: Conforms to Policy 3.9.6.
Charles Plessy
plessy at moszumanska.debian.org
Mon Jan 5 08:23:52 UTC 2015
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 <plessy at debian.org>
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
-
--
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