[med-svn] [bedtools] 03/05: Imported Upstream version 2.19.0
Charles Plessy
plessy at moszumanska.debian.org
Sun Feb 9 12:52:41 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository bedtools.
commit e07e70c36f533ff63055db40c117e5edb2853cab
Author: Charles Plessy <plessy at debian.org>
Date: Sun Feb 9 21:47:29 2014 +0900
Imported Upstream version 2.19.0
---
.gitignore | 9 +
.travis.yml | 5 +
Makefile | 26 +-
README.md | 55 +
README.rst | 47 -
RELEASE_HISTORY | 160 +
data/aluY.chr1.bed.gz | Bin 0 -> 129766 bytes
data/gerp.chr1.bed.gz | Bin 0 -> 1128077 bytes
data/knownGene.hg18.chr21.short.bed | 828 +
data/refseq.chr1.exons.bed.gz | Bin 0 -> 456335 bytes
data/rmsk.hg18.chr21.bed | 57261 -------------------
data/simpleRepeats.chr1.bed.gz | Bin 0 -> 614807 bytes
docs/_static/labibi.css | 54 +
docs/_static/labibi.js | 30 +
docs/bedtools.ai | 1251 +-
docs/conf.py | 17 +-
docs/content/advanced-usage.rst | 129 +-
docs/content/annotateBed.rst | 99 -
docs/content/bamToBed.rst | 88 -
docs/content/bedToIgv.rst | 68 -
docs/content/bedtools-suite.rst | 84 +-
docs/content/complementBed.rst | 48 -
docs/content/example-usage.rst | 330 +-
docs/content/faq.rst | 169 +
docs/content/fastafromBed.rst | 126 -
docs/content/general-usage.rst | 165 +-
docs/content/genomecoverageBed.rst | 122 -
docs/content/groupBy.rst | 194 -
docs/content/images/bedtoolsMenu.png | Bin 0 -> 23256 bytes
docs/content/images/galaxy-bedtools.png | Bin 0 -> 23492 bytes
docs/content/images/github-zip-button.png | Bin 0 -> 45691 bytes
docs/content/images/memory-comparo.png | Bin 0 -> 47395 bytes
docs/content/images/speed-comparo.png | Bin 0 -> 46622 bytes
docs/content/images/tool-glyphs/cluster-glyph.png | Bin 0 -> 45077 bytes
.../images/tool-glyphs/complement-glyph.png | Bin 0 -> 20223 bytes
docs/content/images/tool-glyphs/flank-glyph.png | Bin 0 -> 19718 bytes
.../content/images/tool-glyphs/genomecov-glyph.png | Bin 0 -> 41644 bytes
docs/content/images/tool-glyphs/getfasta-glyph.png | Bin 0 -> 13714 bytes
.../content/images/tool-glyphs/intersect-glyph.png | Bin 0 -> 34437 bytes
docs/content/images/tool-glyphs/jaccard-glyph.ai | 2189 +
docs/content/images/tool-glyphs/jaccard-glyph.png | Bin 0 -> 43088 bytes
docs/content/images/tool-glyphs/map-glyph.png | Bin 0 -> 39209 bytes
docs/content/images/tool-glyphs/map-glyph.svg | 463 +
.../content/images/tool-glyphs/maskfasta-glyph.png | Bin 0 -> 14514 bytes
.../content/images/tool-glyphs/maskfasta-glyph.svg | 171 +
docs/content/images/tool-glyphs/merge-glyph.png | Bin 0 -> 37072 bytes
docs/content/images/tool-glyphs/reldist-glyph.ai | 1137 +
docs/content/images/tool-glyphs/reldist-glyph.png | Bin 0 -> 16670 bytes
docs/content/images/tool-glyphs/reldist-plot.png | Bin 0 -> 206397 bytes
docs/content/images/tool-glyphs/shuffle-glyph.png | Bin 0 -> 31657 bytes
docs/content/images/tool-glyphs/slop-glyph.png | Bin 0 -> 21452 bytes
docs/content/images/tool-glyphs/subtract-glyph.png | Bin 0 -> 23353 bytes
docs/content/images/tool-glyphs/window-glyph.png | Bin 0 -> 25915 bytes
docs/content/installation.rst | 112 +-
docs/content/intersectBed.rst | 385 -
docs/content/maskfastafromBed.rst | 70 -
docs/content/mergeBed.rst | 120 -
docs/content/overview.rst | 239 +-
docs/content/pairToBed.rst | 378 -
docs/content/quick-start.rst | 69 +-
docs/content/related-tools.rst | 67 +
docs/content/shuffleBed.rst | 155 -
docs/content/slopBed.rst | 84 -
docs/content/subtractBed.rst | 88 -
docs/content/tips-and-tricks.rst | 7 +
docs/content/tools/annotate.rst | 120 +
docs/content/tools/bamtobed.rst | 159 +
docs/content/tools/bamtofastq.rst | 103 +
.../{bed12ToBed6.rst => tools/bed12tobed6.rst} | 19 +-
docs/content/tools/bedpetobam.rst | 5 +
docs/content/{bedToBam.rst => tools/bedtobam.rst} | 13 +-
docs/content/{closestBed.rst => tools/closest.rst} | 17 +-
docs/content/tools/cluster.rst | 123 +
docs/content/tools/complement.rst | 62 +
.../{coverageBed.rst => tools/coverage.rst} | 32 +-
docs/content/tools/expand.rst | 5 +
docs/content/tools/flank.rst | 131 +
docs/content/tools/genomecov.rst | 338 +
docs/content/tools/getfasta.rst | 252 +
docs/content/tools/groupby.rst | 237 +
docs/content/tools/igv.rst | 5 +
docs/content/tools/intersect.rst | 670 +
docs/content/tools/jaccard.rst | 110 +
docs/content/{linksBed.rst => tools/links.rst} | 14 +-
docs/content/tools/makewindows.rst | 5 +
docs/content/tools/map.rst | 191 +
docs/content/tools/maskfasta.rst | 115 +
docs/content/tools/merge.rst | 219 +
docs/content/tools/multicov.rst | 98 +
docs/content/tools/multiinter.rst | 5 +
docs/content/tools/nuc.rst | 5 +
docs/content/{ => tools}/overlap.rst | 11 +-
docs/content/tools/pairtobed.rst | 5 +
.../{pairToPair.rst => tools/pairtopair.rst} | 16 +-
docs/content/tools/random.rst | 157 +
docs/content/tools/reldist.rst | 197 +
docs/content/tools/shuffle.rst | 232 +
docs/content/tools/slop.rst | 147 +
docs/content/{sortBed.rst => tools/sort.rst} | 16 +-
docs/content/tools/subtract.rst | 157 +
docs/content/tools/tag.rst | 5 +
.../{unionBedGraphs.rst => tools/unionbedg.rst} | 27 +-
docs/content/tools/window.rst | 210 +
docs/content/windowBed.rst | 157 -
docs/index.rst | 95 +-
docs/templates/page.html | 140 +
docs/templates/sidebar-intro.html | 22 +
docs/themes/rtd/static/rtd.css_t | 3 +
src/annotateBed/annotateBed.cpp | 9 +-
src/bamToBed/bamToBed.cpp | 208 +-
src/bedToBam/Makefile | 2 +-
src/bedToBam/bedToBam.cpp | 2 +-
src/bedToIgv/Makefile | 2 +-
src/bedToIgv/bedToIgv.cpp | 2 +-
src/bedpeToBam/Makefile | 2 +-
src/bedpeToBam/bedpeToBam.cpp | 2 +-
src/bedtools.cpp | 19 +-
src/closestBed/closestBed.cpp | 99 +-
src/closestBed/closestBed.h | 2 +-
src/clusterBed/clusterBed.cpp | 3 +-
src/complementBed/Makefile | 2 +-
src/complementBed/complementBed.h | 2 +-
src/coverageBed/coverageMain.cpp | 2 +-
src/fastaFromBed/fastaFromBed.cpp | 9 +-
src/fastaFromBed/fastaFromBed.h | 3 +-
src/fastaFromBed/fastaFromBedMain.cpp | 9 +-
src/flankBed/Makefile | 2 +-
src/flankBed/flankBed.h | 2 +-
src/genomeCoverageBed/Makefile | 2 +-
src/genomeCoverageBed/genomeCoverageBed.h | 2 +-
src/intersectBed/intersectBed.cpp | 401 -
src/intersectBed/intersectBed.h | 102 -
src/intersectBed/intersectMain.cpp | 326 -
src/intersectFile/Makefile | 45 +
src/intersectFile/intersectFile.cpp | 105 +
src/intersectFile/intersectFile.h | 46 +
src/intersectFile/intersectMain.cpp | 130 +
src/jaccard/jaccard.cpp | 66 +-
src/jaccard/jaccard.h | 6 +-
src/jaccard/jaccardMain.cpp | 7 +-
src/mapBed/mapBed.cpp | 122 -
src/mapFile/Makefile | 56 +
src/mapFile/mapFile.cpp | 120 +
src/{mapBed/mapBed.h => mapFile/mapFile.h} | 55 +-
src/{mapBed => mapFile}/mapMain.cpp | 38 +-
src/mergeBed/mergeBed.cpp | 21 +-
src/mergeBed/mergeBed.h | 16 +-
src/mergeBed/mergeMain.cpp | 36 +-
src/multiIntersectBed/Makefile | 2 +-
src/multiIntersectBed/multiIntersectBed.h | 2 +-
src/multiIntersectBed/multiIntersectBedMain.cpp | 2 +-
src/nekSandbox1/FormatGuess.h | 76 +
src/{mapBed => nekSandbox1}/Makefile | 29 +-
src/nekSandbox1/nekSandboxMain.cpp | 338 +
src/nucBed/nucBed.cpp | 19 +-
src/nucBed/nucBed.h | 3 +-
src/nucBed/nucBedMain.cpp | 27 +-
src/pairToBed/pairToBedMain.cpp | 2 +-
src/randomBed/Makefile | 2 +-
src/randomBed/randomBed.h | 2 +-
src/regressTest/Makefile | 49 +
src/regressTest/RegressTest.cpp | 664 +
src/regressTest/RegressTest.h | 93 +
src/regressTest/regressTestMain.cpp | 67 +
src/{intersectBed => reldist}/Makefile | 8 +-
src/reldist/reldist.cpp | 154 +
src/{jaccard/jaccard.h => reldist/reldist.h} | 38 +-
.../jaccardMain.cpp => reldist/reldistMain.cpp} | 80 +-
src/{intersectBed => sampleFile}/Makefile | 26 +-
src/sampleFile/SampleFile.cpp | 121 +
src/sampleFile/SampleFile.h | 43 +
src/sampleFile/sampleMain.cpp | 77 +
src/shuffleBed/Makefile | 2 +-
src/shuffleBed/shuffleBed.cpp | 167 +-
src/shuffleBed/shuffleBed.h | 12 +-
src/shuffleBed/shuffleBedMain.cpp | 41 +-
src/slopBed/Makefile | 2 +-
src/slopBed/slopBed.h | 2 +-
src/subtractBed/subtractBed.cpp | 25 +-
src/subtractBed/subtractBed.h | 3 +-
src/subtractBed/subtractMain.cpp | 17 +-
src/tagBam/tagBam.cpp | 3 +-
src/tagBam/tagBam.h | 1 -
src/unionBedGraphs/Makefile | 2 +-
src/unionBedGraphs/unionBedGraphs.h | 2 +-
src/unionBedGraphs/unionBedGraphsMain.cpp | 2 +-
src/utils/BamTools/.gitignore | 2 +
src/utils/BamTools/src/api/BamAlignment.h | 5 +-
src/utils/BamTools/src/api/BamReader.cpp | 5 +
src/utils/BamTools/src/api/BamReader.h | 2 +
.../BamTools/src/api/internal/bam/BamReader_p.cpp | 29 +
.../BamTools/src/api/internal/bam/BamReader_p.h | 1 +
.../src/api/internal/io/BamDeviceFactory_p.cpp | 8 +
.../src/api/internal/io/BamDeviceFactory_p.h | 1 +
.../BamTools/src/api/internal/io/BgzfStream_p.cpp | 24 +
.../BamTools/src/api/internal/io/BgzfStream_p.h | 2 +
src/utils/BamTools/src/api/internal/io/NetUnix_p.h | 1 -
.../src/api/internal/io/StdStreamDevice_p.h | 54 +
src/utils/BinTree/BinTree.cpp | 220 +
src/utils/BinTree/BinTree.h | 75 +
src/utils/{fileType => BinTree}/Makefile | 21 +-
src/utils/BlockedIntervals/Makefile | 4 +-
src/utils/Contexts/ContextBase.cpp | 365 +
src/utils/Contexts/ContextBase.h | 236 +
src/utils/Contexts/ContextIntersect.cpp | 318 +
src/utils/Contexts/ContextIntersect.h | 98 +
src/utils/Contexts/ContextMap.cpp | 118 +
src/utils/Contexts/ContextMap.h | 39 +
src/utils/Contexts/ContextSample.cpp | 79 +
src/utils/Contexts/ContextSample.h | 31 +
src/utils/Contexts/Makefile | 42 +
src/utils/Fasta/Fasta.cpp | 37 +-
src/utils/Fasta/Fasta.h | 13 +-
src/utils/Fasta/Makefile | 2 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 100 +
.../FileRecordTools/FileReaders/BamFileReader.h | 67 +
.../FileReaders/BufferedStreamMgr.cpp | 132 +
.../FileReaders/BufferedStreamMgr.h | 53 +
.../FileRecordTools/FileReaders/FileReader.cpp | 33 +
src/utils/FileRecordTools/FileReaders/FileReader.h | 42 +
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 269 +
.../FileRecordTools/FileReaders/InputStreamMgr.h | 74 +
src/utils/FileRecordTools/FileReaders/Makefile | 41 +
.../FileReaders/SingleLineDelimTextFileReader.cpp | 135 +
.../FileReaders/SingleLineDelimTextFileReader.h | 46 +
.../FileReaders/SingleLineDelimTransferBuffer.cpp | 72 +
.../FileReaders/SingleLineDelimTransferBuffer.h | 31 +
src/utils/FileRecordTools/FileRecordMgr.cpp | 398 +
src/utils/FileRecordTools/FileRecordMgr.h | 193 +
src/utils/FileRecordTools/Makefile | 51 +
src/utils/FileRecordTools/Records/BamRecord.cpp | 176 +
src/utils/FileRecordTools/Records/BamRecord.h | 55 +
.../FileRecordTools/Records/Bed12Interval.cpp | 148 +
src/utils/FileRecordTools/Records/Bed12Interval.h | 77 +
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 81 +
src/utils/FileRecordTools/Records/Bed3Interval.h | 43 +
src/utils/FileRecordTools/Records/Bed4Interval.cpp | 62 +
src/utils/FileRecordTools/Records/Bed4Interval.h | 38 +
src/utils/FileRecordTools/Records/Bed5Interval.cpp | 72 +
src/utils/FileRecordTools/Records/Bed5Interval.h | 36 +
src/utils/FileRecordTools/Records/Bed6Interval.cpp | 83 +
src/utils/FileRecordTools/Records/Bed6Interval.h | 36 +
.../FileRecordTools/Records/BedGraphInterval.cpp | 62 +
.../FileRecordTools/Records/BedGraphInterval.h | 36 +
.../FileRecordTools/Records/BedPlusInterval.cpp | 119 +
.../FileRecordTools/Records/BedPlusInterval.h | 54 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 217 +
src/utils/FileRecordTools/Records/BlockMgr.h | 65 +
src/utils/FileRecordTools/Records/GffRecord.cpp | 159 +
src/utils/FileRecordTools/Records/GffRecord.h | 51 +
src/utils/FileRecordTools/Records/Makefile | 45 +
src/utils/FileRecordTools/Records/Record.cpp | 203 +
src/utils/FileRecordTools/Records/Record.h | 155 +
.../FileRecordTools/Records/RecordKeyList.cpp | 68 +
src/utils/FileRecordTools/Records/RecordKeyList.h | 60 +
src/utils/FileRecordTools/Records/RecordMgr.cpp | 277 +
src/utils/FileRecordTools/Records/RecordMgr.h | 47 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 111 +
src/utils/FileRecordTools/Records/VcfRecord.h | 40 +
.../FileRecordTools/Records/recordsTar.tar.gz | Bin 0 -> 54443 bytes
.../genomeFile.cpp => GenomeFile/GenomeFile.cpp} | 4 +-
.../genomeFile.h => GenomeFile/GenomeFile.h} | 2 +-
src/utils/GenomeFile/Makefile | 34 +
src/utils/GenomeFile/NewGenomeFile.cpp | 124 +
src/utils/GenomeFile/NewGenomeFile.h | 65 +
src/utils/NewChromsweep/Makefile | 39 +
src/utils/NewChromsweep/NewChromsweep.cpp | 211 +
src/utils/NewChromsweep/NewChromsweep.h | 96 +
src/utils/RecordOutputMgr/Makefile | 39 +
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 430 +
src/utils/RecordOutputMgr/RecordOutputMgr.h | 72 +
src/utils/VectorOps/VectorOps.cpp | 28 +-
src/utils/VectorOps/VectorOps.h | 8 +-
src/utils/bedFile/bedFile.cpp | 56 +-
src/utils/bedFile/bedFile.h | 16 +
src/utils/bedFilePE/bedFilePE.cpp | 10 +-
src/utils/bedGraphFile/bedGraphFile.cpp | 10 +-
src/utils/bedGraphFile/bedGraphFile.h | 3 +
src/utils/chromsweep/chromsweep.cpp | 2 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 387 +
src/utils/fileType/FileRecordTypeChecker.h | 126 +
src/utils/fileType/Makefile | 20 +-
src/utils/general/BTlist.h | 262 +
src/utils/general/BedtoolsTypes.h | 33 +
src/utils/general/CompressionTools.cpp | 45 +
src/utils/general/CompressionTools.h | 25 +
src/utils/general/DualQueue.h | 124 +
src/utils/general/ErrorMsg.h | 14 +
src/utils/general/FreeList.h | 83 +
src/utils/general/InflateStreamBuf.h | 130 +
src/utils/{fileType => general}/Makefile | 17 +-
src/utils/general/ParseTools.cpp | 143 +
src/utils/general/ParseTools.h | 97 +
src/utils/general/PushBackStreamBuf.cpp | 51 +
src/utils/general/PushBackStreamBuf.h | 39 +
src/utils/general/QuickString.cpp | 230 +
src/utils/general/QuickString.h | 72 +
src/utils/genomeFile/Makefile | 32 -
src/utils/tabFile/tabFile.cpp | 15 +-
src/utils/version/version_release.txt | 6 +-
src/windowBed/windowMain.cpp | 2 +-
src/windowMaker/Makefile | 2 +-
src/windowMaker/windowMaker.h | 2 +-
test/bamtobed/test-bamtobed.sh | 65 +-
test/bamtobed/two_blocks_w_D.sam | 6 +
test/bed12tobed6/test-bed12tobed6.sh | 2 +-
test/closest/close-a.bed | 8 +
test/closest/close-b.bed | 7 +
test/closest/strand-test-a.bed | 2 +
test/closest/strand-test-b.bed | 3 +
test/closest/test-closest.sh | 88 +-
test/cluster/test-cluster.sh | 2 +-
test/coverage/test-coverage.sh | 2 +-
test/expand/test-expand.sh | 2 +-
test/flank/test-flank.sh | 2 +-
test/general/empty.bed | 0
test/general/non-empty.bed.gz | Bin 0 -> 53 bytes
test/general/test-general.sh | 33 +-
test/genomecov/test-genomecov.sh | 2 +-
test/getfasta/t_fH.fa | 6 +
test/getfasta/t_fH.fa.fai | 1 +
test/getfasta/test-getfasta.sh | 42 +-
test/groupBy/test-groupby.sh | 14 +-
test/intersect/a.bam | Bin 0 -> 1739 bytes
test/intersect/aVSb.bam | Bin 0 -> 1735 bytes
test/intersect/aWithHeaderVsB.txt | 4002 ++
test/intersect/a_bgzipped.bed.gz | Bin 0 -> 85 bytes
test/intersect/a_gzipped.bed.gz | Bin 0 -> 63 bytes
test/intersect/a_withLargeHeader.bed | 4002 ++
test/intersect/a_withLargeHeader_bgzipped.bed.gz | Bin 0 -> 10624 bytes
test/intersect/a_withLargeHeader_gzipped.bed.gz | Bin 0 -> 10384 bytes
test/intersect/a_with_bothUnmapped.bam | Bin 0 -> 2911 bytes
test/intersect/bed3.bed | 1 +
test/intersect/bed4.bed | 1 +
test/intersect/bed5.bed | 1 +
test/intersect/bed6.bed | 1 +
test/intersect/bed6.strand.bed | 1 +
test/intersect/bed6.strand2.bed | 2 +
test/intersect/bedplus.bed | 1 +
test/intersect/chromOrderA.bed | 6 +
test/intersect/chromOrderB.bed | 12 +
test/intersect/chromsOutOfOrder.bed | 4 +
test/intersect/d.bed | 1 +
test/intersect/gdc.bam | Bin 0 -> 204 bytes
test/intersect/gdc.gff | 12 +
test/intersect/gdc_exp | 12 +
test/intersect/gdc_one.bed | 1 +
test/intersect/human.hg19.genome | 94 +
test/intersect/human.hg19.vSort.genome | 93 +
test/intersect/j1.bed | 1 +
test/intersect/new_test-intersect.sh | 668 +
test/intersect/oneUnmapped.bam | Bin 0 -> 2564 bytes
test/intersect/performanceTest.sh | 138 +
.../queryUnmappedMateMappedCoordsInvalid.bam | Bin 0 -> 1051 bytes
test/intersect/recordsOutOfOrder.bed | 4 +
test/intersect/test-intersect.sh | 152 +-
test/intersect/three_blocks_match.bam | Bin 0 -> 1804 bytes
test/intersect/two_blocks_partial.bam | Bin 0 -> 1805 bytes
test/intersect/two_blocks_partial.bed | 1 +
test/jaccard/test-jaccard.sh | 46 +-
test/map/a.vsorted.bed | 5 +
test/map/b.vsorted.bed | 3 +
test/map/genome | 3 +
test/map/ivls.bed | 1 +
test/map/ivls2.bed | 3 +
test/map/t.bed | 1 +
test/map/test-map.sh | 553 +-
test/map/test.gff | 7 +
test/map/test.vcf | 26 +
test/map/three_blocks_match.bed | 1 +
test/map/three_blocks_nomatch.bed | 1 +
test/map/values.bam | Bin 0 -> 1825 bytes
test/map/values.bed | 2 +-
test/map/values4.bed | 12 +
test/map/values5.bed | 8 +
test/merge/test-merge.sh | 30 +-
test/multicov/test-multicov.sh | 2 +-
test/reldist/test-reldist.sh | 149 +
test/sample/human.hg19.genome | 94 +
test/sample/sample_help_withoutVersion.txt | 33 +
test/sample/test-sample.sh | 124 +
test/slop/test-slop.sh | 2 +-
test/subtract/c.bed | 1 +
test/subtract/d.bed | 2 +
test/subtract/test-subtract.sh | 22 +-
test/test.sh | 41 +-
386 files changed, 33980 insertions(+), 62180 deletions(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..d831ebb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,9 @@
+*.o
+testingData
+*.pdf
+bin/*
+obj/*
+docs/_build/
+src/utils/version/version_git.h
+.project
+.cproject
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..23ffa85
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,5 @@
+language: cpp
+compiler:
+ - gcc
+ - clang
+script: make test
diff --git a/Makefile b/Makefile
index 28c934a..139988b 100644
--- a/Makefile
+++ b/Makefile
@@ -16,11 +16,11 @@ export BIN_DIR = bin
export SRC_DIR = src
export UTIL_DIR = src/utils
export CXX = g++
-ifeq ($(DEBUG),1)
-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
-else
+#ifeq ($(DEBUG),1)
+#export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+#else
export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC
-endif
+#endif
export LIBS = -lz
export BT_ROOT = src/utils/BamTools/
@@ -42,18 +42,22 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/genomeCoverageBed \
$(SRC_DIR)/getOverlap \
$(SRC_DIR)/groupBy \
- $(SRC_DIR)/intersectBed \
+ $(SRC_DIR)/intersectFile \
$(SRC_DIR)/jaccard \
$(SRC_DIR)/linksBed \
$(SRC_DIR)/maskFastaFromBed \
- $(SRC_DIR)/mapBed \
+ $(SRC_DIR)/mapFile \
$(SRC_DIR)/mergeBed \
$(SRC_DIR)/multiBamCov \
$(SRC_DIR)/multiIntersectBed \
+ $(SRC_DIR)/nekSandbox1 \
$(SRC_DIR)/nucBed \
$(SRC_DIR)/pairToBed \
$(SRC_DIR)/pairToPair \
$(SRC_DIR)/randomBed \
+ $(SRC_DIR)/regressTest \
+ $(SRC_DIR)/reldist \
+ $(SRC_DIR)/sampleFile \
$(SRC_DIR)/shuffleBed \
$(SRC_DIR)/slopBed \
$(SRC_DIR)/sortBed \
@@ -64,12 +68,17 @@ SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/windowMaker
UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
+ $(SRC_DIR)/utils/BinTree \
$(SRC_DIR)/utils/version \
$(SRC_DIR)/utils/bedGraphFile \
$(SRC_DIR)/utils/chromsweep \
+ $(SRC_DIR)/utils/Contexts \
+ $(SRC_DIR)/utils/FileRecordTools \
+ $(SRC_DIR)/utils/general \
$(SRC_DIR)/utils/gzstream \
$(SRC_DIR)/utils/fileType \
$(SRC_DIR)/utils/bedFilePE \
+ $(SRC_DIR)/utils/NewChromsweep \
$(SRC_DIR)/utils/sequenceUtilities \
$(SRC_DIR)/utils/tabFile \
$(SRC_DIR)/utils/BamTools \
@@ -77,7 +86,8 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
$(SRC_DIR)/utils/BlockedIntervals \
$(SRC_DIR)/utils/Fasta \
$(SRC_DIR)/utils/VectorOps \
- $(SRC_DIR)/utils/genomeFile
+ $(SRC_DIR)/utils/GenomeFile \
+ $(SRC_DIR)/utils/RecordOutputMgr
BUILT_OBJECTS = $(OBJ_DIR)/*.o
@@ -85,7 +95,7 @@ BUILT_OBJECTS = $(OBJ_DIR)/*.o
all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
@echo "- Building main bedtools binary."
@$(CXX) $(CXXFLAGS) -c src/bedtools.cpp -o obj/bedtools.o -I$(UTIL_DIR)/version/
- @$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
+ @$(CXX) $(CXXFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS)
@echo "done."
@echo "- Creating executables for old CLI."
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..55042d8
--- /dev/null
+++ b/README.md
@@ -0,0 +1,55 @@
+
+bedtools - a swiss army knife for genome arithmetic
+===================================================
+
+**Current version**: 2.18.2
+
+Note
+-------
+Stable release for bedtools were formerly archived on Google Code. Unfortunately, the Google Code
+downloads facility is shutting down; so henceforth, all source code and stable releases will be
+maintained via this Github repository.
+
+Summary
+-------
+Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
+
+While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
+
+
+Performance
+-----------
+As of version 2.18, ``bedtools`` is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are pre-sorted
+by chromosome and start position. As you can see in the plots below, the speed and memory consumption scale nicely
+with sorted data as compared to the poor scaling for unsorted data. The current version of bedtools intersect is as fast as (or slightly faster) than the ``bedops`` package's ``bedmap`` which uses a similar algorithm for sorted data. The plots below represent counting the number of intersecting alignments from exome capture BAM files against CCDS exons.
+The alignments have been converted to BED to facilitate comparisons to ``bedops``. We compare to the bedmap ``--ec`` option because similar error checking is enforced by ``bedtools``.
+
+
+**Note:** bedtools could not complete when using 100 million alignments and the R-Tree algorithm used for unsorted data.
+
+
+
+
+
+
+Details
+-------
+First created through urgency and adrenaline by Aaron Quinlan Spring 2009.
+Maintained by the Quinlan Laboratory at the University of Virginia.
+
+1. **Lead developers**: Aaron Quinlan, Neil Kindlon
+2. **Significant contributions**: Assaf Gordon, Royden Clark, John Marshall, Brent Pedersen, Ryan Dale
+3. **Repository**: https://github.com/arq5x/bedtools2
+4. **Stable releases**: https://github.com/arq5x/bedtools2/releases
+5. **Documentation**: http://bedtools.readthedocs.org
+6. **License**: Released under GNU public license version 2 (GPL v2).
+
+
+Citation
+--------
+*Please cite the following article if you use BEDTools in your research*:
+ * Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
+
+Also, if you use *pybedtools*, please cite the following.
+ * Dale RK, Pedersen BS, and Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (2011). doi:10.1093/bioinformatics/btr539
+
diff --git a/README.rst b/README.rst
deleted file mode 100644
index 4aae255..0000000
--- a/README.rst
+++ /dev/null
@@ -1,47 +0,0 @@
-==============================
- BEDTools
-==============================
-
-Created by Aaron Quinlan Spring 2009.
-
-Copyright 2009,2010,2011 Aaron Quinlan. All rights reserved.
-
-Stable releases: http://code.google.com/p/bedtools
-
-Repository: https://github.com/arq5x/bedtools
-
-Released under GNU public license version 2 (GPL v2).
-
-
-Summary
--------
-BEDTools is a collection of utilities for comparing, summarizing, and
-intersecting genomic features in BED, GTF/GFF, VCF and BAM formats.
-
-
-Manual
-------
-See the extensive PDF manual included at: http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf.
-
-This manual covers many common usage examples. There are also examples available at:
-http://code.google.com/p/bedtools/wiki/Usage
-http://code.google.com/p/bedtools/wiki/UsageAdvanced
-
-Installation
-------------
-Git
-...
-git clone git://github.com/arq5x/bedtools.git
-
-Download tarball - that big gray button on the upper right.
-...........................................................
-1. Unpack the source downloaded tarball.
-2. cd into the expanded folder.
-3. Type "make" and hit enter.
-4. If you encountered no errors, then bedtools should now be in bin/
- If not, try to troubleshoot then email me: aaronquinlan at gmail dot com
-5. Run the test suite with: "make test"
-6. Copy the files in bin/ to ~/bin or if you have the privileges, to /usr/local/bin. Make sure that the directory to which you copy the tools is in your $PATH
-7. Use the tools.
-
-
diff --git a/RELEASE_HISTORY b/RELEASE_HISTORY
index bb93096..b7c34f3 100644
--- a/RELEASE_HISTORY
+++ b/RELEASE_HISTORY
@@ -1,3 +1,163 @@
+Version 2.18.1 (16-Dec-2013)
+
+Fixes that address compilation errors with CLANG and force compilation of custom BamTools library.
+
+
+Version 2.18.0 (13-Dec-2013)
+
+The Google Code site is deprecated
+----------------------------------
+It looks like the Google Code service is going the way of the venerable Google Reader. As such, we are moving the repository and all formal release tarballs to Github. We have started a new repository prosaically named "bedtools2". The original bedtools repository will remain for historical purposes, but we created a new repository to distinguish the two code bases as they will become rather different over time.
+
+[https://github.com/arq5x/bedtools2](https://github.com/arq5x/bedtools2)
+
+
+We gutted the core API and algorithms
+-------------------------------------
+
+Much of Neil's hard work has been devoted to completely rewriting the core file/stream writing API to be much more flexible in the adoption of new formats. In addition, he has substantially improved many of the core algorithms for detecting interval intersections.
+
+
+Improved performance
+--------------------
+
+The 2.18.0 release leverages these improvements in the "intersect" tool. Forthcoming releases will see the new API applied to other tools, but we started with intersect as it is the most widely used tool in the suite.
+
+**Performance with sorted datasets.** The "chromsweep" algorithm we use for detecting intersections is now **60 times
+faster** than when it was first release in version 2.16.2, and is **** than the 2.17 release. This makes the
+algorithm slightly faster
+that the algorithm used in the bedops ``bedmap`` tool. As an example, the following [figure](https://dl.dropboxusercontent.com/u/515640/bedtools-intersect-sorteddata.png) demonstrates the speed
+when intersecting GENCODE exons against 1, 10, and 100 million BAM alignments from an exome capture experiment.
+Whereas in version 2.16.2 this wuld have taken 80 minutes, **it now takes 80 seconds**.
+
+**Greater flexibility.** In addition, BAM, BED, GFF/GTF, or VCF files are now automatically detected whether they are a file, stream, or FIFO in either compressed or uncompressed form. As such, one now longer has specify `-abam` when using BAM input as the "A" file with ``intersect``. Moreover, any file type can be used for either the A or
+the B file.
+
+
+Better support for different chromosome sorting criteria
+--------------------------------------------------------
+Genomic analysis is plagued by different chromosome naming and sorting conventions. Prior to this release,
+the ``-sorted`` option in the ``intersect`` tool required that the chromosomes were sorted in alphanumeric
+order (e.g. chr1, chr10, etc. or 1, 10, etc.). Starting with this release, we now simply require by default
+that the records are **GROUPED** by chromosome and that within each chromosome group, the records are sorted by
+chromosome position. This will allow greater flexibility.
+
+One problem that can arise however, is if two different files are each grouped by chromosome, yet the two
+files follow a different chromosome order. In order to detect and enforce the same order, one can explicitly
+state the expected chromosome order through the use of a genome (aka chromsizes) file. Please see the
+documentation [here](http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html#sorted-invoke-a-memory-efficient-algorithm-for-very-large-files) and [here](http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html#g-define-an-alternate-chromosome-sort-order-via-a-genome-file) for examples.
+
+
+New tools
+---------
+1. The ``jaccard`` tool. While not exactly new, there have been improvements to the tool and there is finally
+documentation. Read more here: http://bedtools.readthedocs.org/en/latest/content/tools/jaccard.html
+
+2. The ``reldist`` tool. Details here: http://bedtools.readthedocs.org/en/latest/content/tools/reldist.html
+
+3. The ``sample`` tool. Uses reservoir sampling to randomly sample a specified number of records from BAM, BED,
+VCF, and GFF/GTF files.
+
+
+Enhancements
+------------
+1. Improvements in the consistency of the output of the ``merge`` tool. Thanks to @kcha.
+2. A new ``-allowBeyondChromEnd`` option in the ``shuffle`` tool. Thanks to @stephenturner.
+[docs](http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html#allowbeyondchromend-allow-records-to-extend-beyond-the-chrom-length)
+3. A new ``-noOverlapping`` option that prevents shuffled intervals from overlapping one another. Thanks to @brentp. [docs](http://bedtools.readthedocs.org/en/latest/content/tools/shuffle.html#nooverlapping-prevent-shuffled-intervals-from-overlapping)
+4. Allow the user to specify the maximum number of shuffling attempts via the ``-maxTries`` option in the ``shuffle`` tool.
+4. Various improvements to the documentation provided by manu different users. Thanks to all.
+5. Added the number of intersections (``n_intersections``) to the Jaccard output. Thanks to @brentp.
+6. Various improvements to the ``tag`` tool.
+7. Added the ``-N`` (remove any) option to the ``subtract`` tool.
+
+
+
+
+Version 2.17.0 (3-Nov-2012)
+=====================
+=== New Tool ===
+=====================
+
+We have added a new tool (bedtools "jaccard") for measuring the Jaccard statistic
+between two interval files. The Jaccard stat measures the ratio of the length
+of the intersection over the length of the union of the two sets. In this
+case, the union is measured as the sum of the lengths of the intervals in each
+set minus the length of the intersecting intervals. As such, the Jaccard
+statistic provides a "distance" measure between 0 (no intersections)
+and 1 (self intersection). The higher the score, the more the two sets of
+intervals overlap one another. This tool was motivated by Favorov et al, 2012.
+For more details, see see PMID: 22693437.
+
+We anticipate releasing other statistical measures in forthcoming releases.
+
+
+
+===================================
+=== New Features & enhancements ===
+===================================
+1. The genome file drives the BAM header in "bedtools bedtobam"
+
+2. Substantially improvement the performance of the -sorted option in
+ "bedtools intersect" and "bedtools map". For many applications,
+ bedtools is now nearly as fast as the BEDOPS suite when intersecting
+ pre-sorted data. This improvement is thanks to Neil Kindlon, a staff
+ scientist in the Quinlan lab.
+
+3. Tightened the logic for handling split (blocked) BAM and BED records
+
+4. Added ranged column selection to "bedtools groupby". Thanks to Brent Pedersen"
+ - e.g., formerly "bedtools groupby -g 1,2,3,4,5"; now "-g 1-5"
+
+5. "bedtools getfasta" now properly extracts sequences based on blocked (BED12)
+ records (e.g., exons from genes in BED12 format).
+
+6. "bedtools groupby" now allows a header line in the input.
+
+7. With -N, the user can now force the closest interval to have a different name
+ field in "bedtools closest"
+
+8. With -A, the user can now force the subtraction of entire interval when
+ any overlap exists in "bedtools subtract".
+
+9. "bedtools shuffle" can now shuffle BEDPE records.
+
+10. Improved random number generation.
+
+11. Added -split, -s, -S, -f, -r options to "bedtools multicov"
+
+12. Improvements to the regression testing framework.
+
+13. Standardized the tag reporting logic in "bedtools bamtobed"
+
+14. Improved the auto-detection of VCF format. Thanks to Michael James Clark.
+
+====================
+=== Bug fixes ===
+====================
+1. Fixed a bug in bedtobam's -bed12 mode.
+
+2. Properly include unaligned BAM alignments with "bedtools intersect"'s -v option.
+
+3. Fixed off by one error in "bedtools closest"'s -d option
+
+4."bedtools bamtobed" fails properly for non-existent file.
+
+5. Corrected missing tab in "bedtools annotate"'s header.
+
+6. Allow int or uint tags in "bedtools bamtobed"
+
+7. "bedtools flank" no longer attempts to take flanks prior to the start of a
+ chromosome.
+
+8. Eliminated an extraneous tab from "bedtools window" -c.
+
+9. Fixed a corner case in the -sorted algorithm.
+
+10.Prevent numeric overflow in "bedtools coverage -hist"
+
+
+
Version 2.14.1-3 (2-Nov-2011)
Bug Fixes
diff --git a/data/aluY.chr1.bed.gz b/data/aluY.chr1.bed.gz
new file mode 100644
index 0000000..8e03a62
Binary files /dev/null and b/data/aluY.chr1.bed.gz differ
diff --git a/data/gerp.chr1.bed.gz b/data/gerp.chr1.bed.gz
new file mode 100644
index 0000000..d8a7e6b
Binary files /dev/null and b/data/gerp.chr1.bed.gz differ
diff --git a/data/knownGene.hg18.chr21.short.bed b/data/knownGene.hg18.chr21.short.bed
new file mode 100644
index 0000000..808943c
--- /dev/null
+++ b/data/knownGene.hg18.chr21.short.bed
@@ -0,0 +1,828 @@
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diff --git a/data/refseq.chr1.exons.bed.gz b/data/refseq.chr1.exons.bed.gz
new file mode 100644
index 0000000..adbc418
Binary files /dev/null and b/data/refseq.chr1.exons.bed.gz differ
diff --git a/data/rmsk.hg18.chr21.bed b/data/rmsk.hg18.chr21.bed
deleted file mode 100755
index 616997c..0000000
--- a/data/rmsk.hg18.chr21.bed
+++ /dev/null
@@ -1,57261 +0,0 @@
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-chr21 9942802 9942913 Charlie9 382 -
-chr21 9943444 9943603 MER96B 622 -
-chr21 9943950 9944046 AluSg/x 580 -
-chr21 9944161 9944385 L1M5 303 +
-chr21 9944381 9944789 L1PA15-16 2435 +
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-chr21 9949412 9949448 (CA)n 324 +
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-chr21 9953020 9953097 MADE2 345 -
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-chr21 9962307 9962600 AluSx 1885 -
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-chr21 10047184 10047394 L1M5 1898 +
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-chr21 14195531 14195630 MSTA 262 -
-chr21 14195630 14197194 MSTA-int 5457 -
-chr21 14197197 14197329 MST-int 512 +
-chr21 14197363 14197647 MSTA 1229 -
-chr21 14197652 14197894 THE1-int 798 +
-chr21 14197882 14197938 THE1-int 301 -
-chr21 14198050 14198154 MSTA-int 318 -
-chr21 14198151 14198293 MST-int 456 +
-chr21 14198318 14198702 MSTA 1284 -
-chr21 14198702 14198953 MSTA-int 1370 -
-chr21 14198950 14199188 MSTA-int 1334 -
-chr21 14199217 14199554 MSTA 1316 -
-chr21 14202319 14202378 (TG)n 189 +
-chr21 14202705 14202806 HSAT5 271 +
-chr21 14203102 14203186 HSAT5 296 +
-chr21 14203769 14203859 L1PA17 231 +
-chr21 14203856 14204314 L1MC4 1277 +
-chr21 14205172 14205254 L2 250 -
-chr21 14205878 14205899 AT_rich 21 +
-chr21 14206261 14206555 AluSc 2107 +
-chr21 14206715 14207378 L1PA16 4437 -
-chr21 14207378 14207401 (TTTA)n 207 +
-chr21 14207401 14207853 L1PA16 4437 -
-chr21 14207890 14208190 AluSx 2001 -
-chr21 14208368 14208677 AluSg1 1960 -
-chr21 14208708 14209005 AluSg 2082 +
-chr21 14209955 14210056 L1MA9 378 +
-chr21 14212482 14212777 AluJo 1437 +
-chr21 14212890 14214006 L1MA5 2941 +
-chr21 14214007 14214265 AluJo 965 +
-chr21 14214332 14214608 L1MA5 1323 +
-chr21 14214645 14215024 MLT1G1 727 +
-chr21 14216369 14216503 L1MB8 440 +
-chr21 14216503 14216550 MER7D 242 +
-chr21 14216570 14217433 L1MB8 2412 +
-chr21 14217442 14217853 MER61C 2384 +
-chr21 14217853 14218176 L1MB8 1230 +
-chr21 14218396 14218760 MER4E1 1202 +
-chr21 14218856 14219336 L1PA10 3238 +
-chr21 14219722 14220048 AluSq 1921 -
-chr21 14220565 14220594 AT_rich 22 +
-chr21 14220599 14220669 MER34C 390 -
-chr21 14220929 14221215 AluSg 1627 +
-chr21 14222482 14222790 AluSg 2117 -
-chr21 14223139 14223450 AluSx 2244 -
-chr21 14223879 14224038 AluJb 1366 -
-chr21 14224038 14224063 (TTTA)n 225 +
-chr21 14224063 14224183 AluJb 1366 -
-chr21 14224202 14224262 MIR 192 +
-chr21 14225285 14225778 L1MB8 1846 +
-chr21 14226842 14226920 L2 269 +
-chr21 14227634 14227909 L1MB7 977 -
-chr21 14228444 14229810 SVA 5514 -
-chr21 14229854 14231191 SVA 2793 -
-chr21 14233259 14233282 AT_rich 23 +
-chr21 14234211 14234232 AT_rich 21 +
-chr21 14234281 14234562 L1MC 512 -
-chr21 14234666 14234983 AluSq 1998 +
-chr21 14235171 14235219 AT_rich 34 +
-chr21 14235295 14235333 AT_rich 24 +
-chr21 14236993 14237079 L1PA5 634 -
-chr21 14239076 14239109 AT_rich 26 +
-chr21 14239363 14239410 AT_rich 26 +
-chr21 14239799 14240097 AluJo 1428 +
-chr21 14240318 14240358 L2 211 -
-chr21 14240640 14240942 AluSx 1927 -
-chr21 14241405 14241691 AluSp 1917 -
-chr21 14243311 14243347 AT_rich 22 +
-chr21 14243459 14243762 AluSx 1859 +
-chr21 14244758 14244804 (CA)n 244 +
-chr21 14246975 14247097 MER5A1 429 +
-chr21 14247926 14248219 AluY 2336 -
-chr21 14248415 14248711 AluJo 1228 -
-chr21 14248745 14249027 AluJb 1552 +
-chr21 14249413 14250184 L1PA5 6381 +
-chr21 14250418 14250474 AT_rich 21 +
-chr21 14250570 14250853 AluJb 1208 +
-chr21 14251039 14251357 AluSx 1845 -
-chr21 14251610 14251717 FLAM_A 640 -
-chr21 14253016 14253045 AT_rich 22 +
-chr21 14253993 14254089 MIRb 197 +
-chr21 14254709 14254949 MIRb 254 +
-chr21 14255101 14255226 FLAM_A 615 +
-chr21 14255672 14255829 MER21A 701 -
-chr21 14255830 14255964 Tigger7 859 +
-chr21 14256980 14257425 L1MC1 2371 +
-chr21 14257435 14257728 AluSq 1858 +
-chr21 14257765 14257793 AT_rich 28 +
-chr21 14257793 14258104 AluSx 2135 +
-chr21 14258227 14258254 AT_rich 27 +
-chr21 14258585 14258622 AT_rich 23 +
-chr21 14258655 14259196 MER68 2576 +
-chr21 14259562 14259866 AluJb 1261 +
-chr21 14259947 14260000 FRAM/FAM 387 +
-chr21 14260000 14260086 FAM 493 +
-chr21 14260406 14260448 (TATATG)n 188 +
-chr21 14260462 14260701 Zaphod2 888 +
-chr21 14260701 14261126 Tigger2a 2092 +
-chr21 14261126 14261147 Zaphod2 888 +
-chr21 14261395 14261417 AT_rich 22 +
-chr21 14261834 14262039 MIRb 215 +
-chr21 14262681 14262787 U6 593 -
-chr21 14262903 14262924 AT_rich 21 +
-chr21 14263735 14263853 FLAM_C 648 +
-chr21 14264787 14265074 AluSc 2125 +
-chr21 14265773 14265882 L2 188 +
-chr21 14266545 14266566 AT_rich 21 +
-chr21 14266944 14267182 Charlie8 422 -
-chr21 14268069 14268107 (TG)n 342 +
-chr21 14268113 14268207 FLAM_A 355 -
-chr21 14268219 14268343 MER5A 240 +
-chr21 14270029 14270231 MIR 517 +
-chr21 14270235 14270530 AluJo 1633 -
-chr21 14270630 14270772 MER104 446 +
-chr21 14271235 14271283 L2 219 +
-chr21 14271360 14271414 AT_rich 33 +
-chr21 14271992 14272136 L1M5 237 -
-chr21 14272338 14272463 (TA)n 256 +
-chr21 14272475 14272786 AluSx 2122 +
-chr21 14272832 14272863 AT_rich 24 +
-chr21 14274629 14276513 REP522 2163 +
-chr21 14276513 14277810 L1M1 7141 -
-chr21 14277810 14278281 REP522 1263 +
-chr21 14278850 14278992 REP522 515 -
-chr21 14279130 14279285 (CCCTG)n 255 +
-chr21 14279441 14279567 (CCCTG)n 190 +
-chr21 14279574 14279766 (GCCTG)n 293 +
-chr21 14279785 14279988 (CCCTG)n 342 +
-chr21 14280052 14280131 (CCCTAG)n 268 +
-chr21 14280159 14280260 (CCCTG)n 231 +
-chr21 14280372 14280539 (CCCTG)n 328 +
-chr21 14280474 14280645 (CCCTAG)n 413 +
-chr21 14280564 14280769 (CCCTG)n 304 +
-chr21 14280817 14281006 (CCCTG)n 331 +
-chr21 14280930 14281089 (CCCTAG)n 440 +
-chr21 14281049 14281245 (CCCTG)n 378 +
-chr21 14281277 14281445 (CCCTG)n 311 +
-chr21 14281486 14281664 (CCCTG)n 369 +
-chr21 14281719 14281868 (CCCTG)n 227 +
-chr21 14281892 14282014 (CCCTG)n 314 +
-chr21 14282045 14282260 L1MB7 1031 -
-chr21 14282344 14282641 AluSp 2151 -
-chr21 14282674 14282859 AluSg/x 1201 +
-chr21 14283020 14283464 L1MC4a 519 -
-chr21 14283465 14283658 L1MA9 947 +
-chr21 14283893 14284358 L1ME1 1722 +
-chr21 14284377 14289790 L1P2 25676 -
-chr21 14290068 14290685 L1MB3 2655 -
-chr21 14290694 14290928 L1MD 304 -
-chr21 14290928 14291232 AluSg 2234 -
-chr21 14291232 14291337 L1MD 304 -
-chr21 14291369 14293299 L1M4 10638 -
-chr21 14293299 14293592 AluSx 1906 -
-chr21 14293592 14294219 L1M4 10638 -
-chr21 14294552 14294847 AluSx 1965 +
-chr21 14296670 14296721 AT_rich 23 +
-chr21 14296915 14297206 AluSq 2114 +
-chr21 14297248 14297453 L1M5 238 +
-chr21 14297546 14297855 AluSg1 2002 +
-chr21 14297868 14298152 AluY 2310 +
-chr21 14298152 14298182 (CAA)n 195 +
-chr21 14300097 14300409 MER33 1383 -
-chr21 14300418 14300638 MER58A 1129 -
-chr21 14300816 14301045 L1M5 746 +
-chr21 14301052 14301286 AluSq 1686 +
-chr21 14302007 14302143 MIR 235 +
-chr21 14304922 14304966 (TCCC)n 267 +
-chr21 14310597 14310893 AluSg 2204 +
-chr21 14310904 14311208 AluSx 1858 +
-chr21 14311814 14311948 AluSq/x 1032 -
-chr21 14311950 14312268 AluSx 1965 -
-chr21 14312396 14312536 L2 254 +
-chr21 14312815 14313122 AluJo 1422 -
-chr21 14313122 14313144 AT_rich 22 +
-chr21 14315015 14315303 AluSg 1913 -
-chr21 14315716 14315773 AT_rich 29 +
-chr21 14317714 14317808 MER5A1 363 +
-chr21 14318093 14318301 L1ME3A 374 +
-chr21 14318536 14318602 L2 187 +
-chr21 14318790 14318937 MER5B 490 -
-chr21 14319491 14319581 MIRb 219 +
-chr21 14319619 14320038 MLT1H 1079 +
-chr21 14320695 14320844 MER33 541 +
-chr21 14320844 14321135 AluSg 1790 -
-chr21 14321135 14321207 MER33 541 +
-chr21 14322128 14322524 MER93a 1378 -
-chr21 14323632 14324064 MER92B 742 -
-chr21 14324119 14324439 MER21C 1114 +
-chr21 14325183 14325351 MER67C 1616 +
-chr21 14325351 14325398 (TG)n 402 +
-chr21 14325398 14325779 LTR70 3056 +
-chr21 14325779 14326095 AluY 2370 -
-chr21 14326095 14326603 LTR70 3056 +
-chr21 14328115 14328414 AluSq 2155 +
-chr21 14328645 14328777 MIR 254 +
-chr21 14329209 14329364 MER5A1 501 +
-chr21 14330952 14331504 L3 669 -
-chr21 14331674 14332012 THE1A 2041 -
-chr21 14332208 14332307 MIRm 184 +
-chr21 14332746 14332867 MER117 239 -
-chr21 14333849 14334017 LTR33 603 -
-chr21 14335047 14335653 L1PA14 4418 -
-chr21 14336104 14336565 L1MEc 1154 +
-chr21 14336582 14337749 L1MEc 3036 +
-chr21 14337749 14338193 LTR54B 2312 +
-chr21 14338193 14338582 L1MEc 4138 +
-chr21 14338582 14338873 AluSq 2135 +
-chr21 14338873 14340477 L1MEc 4138 +
-chr21 14340501 14340776 L1MCb 836 +
-chr21 14340791 14341163 L1MCb 1097 +
-chr21 14341166 14341318 AluSp 1097 +
-chr21 14341318 14341380 (GAGTG)n 362 +
-chr21 14341383 14341735 L1MCb 1329 +
-chr21 14341735 14341777 U2 245 -
-chr21 14341777 14342009 L1MCb 1329 +
-chr21 14342015 14342544 L1MCb 2171 +
-chr21 14342586 14343122 LTR55 1944 -
-chr21 14343215 14343900 L1MCb 1989 +
-chr21 14343903 14344702 L1MCb 3261 +
-chr21 14344781 14345114 L1MCb 1602 +
-chr21 14345114 14345394 AluJo 1515 +
-chr21 14345394 14345682 L1MCb 1602 +
-chr21 14345723 14345969 L1ME1 573 +
-chr21 14345968 14346879 L1ME1 2077 +
-chr21 14346994 14347409 L1PA13 2255 -
-chr21 14347417 14347567 AluSq/x 1140 -
-chr21 14347568 14347642 L1P3 499 -
-chr21 14347642 14347780 AluSg/x 1010 +
-chr21 14347780 14348674 L1PREC2 5692 -
-chr21 14348681 14348896 AluSx 1369 -
-chr21 14348943 14349122 (CAGGG)n 366 +
-chr21 14349129 14349207 (CCCTG)n 219 +
-chr21 14349262 14349395 AluSq/x 946 -
-chr21 14349399 14349577 MIR 436 +
-chr21 14349698 14349870 (CCCTAG)n 398 +
-chr21 14349955 14350263 (CTAGGG)n 307 +
-chr21 14350312 14350508 (CAGGG)n 435 +
-chr21 14350526 14350954 (CTAGGG)n 307 +
-chr21 14350989 14351161 (CTAGGG)n 302 +
-chr21 14351167 14351253 (CAGGG)n 254 +
-chr21 14351467 14351626 (CTAGGG)n 380 +
-chr21 14351536 14351763 (CAGGG)n 385 +
-chr21 14351820 14352115 (CTAGGG)n 434 +
-chr21 14352143 14352327 (CAGGG)n 249 +
-chr21 14352340 14352441 (CAGGG)n 189 +
-chr21 14352469 14352542 (CTAGGG)n 247 +
-chr21 14352591 14352788 (CAGGG)n 316 +
-chr21 14352903 14352956 (CAGGC)n 182 +
-chr21 14353037 14353163 (CAGGG)n 211 +
-chr21 14353172 14353326 (CAGGC)n 227 +
-chr21 14353365 14353497 (CAGGG)n 221 +
-chr21 14353622 14353777 REP522 379 +
-chr21 14354346 14354821 REP522 1164 -
-chr21 14354821 14356121 L1M1 6693 +
-chr21 14356121 14357962 REP522 2079 +
-chr21 14359101 14359428 L1M5 328 +
-chr21 14359755 14359784 AT_rich 22 +
-chr21 14359822 14359867 (TA)n 405 +
-chr21 14359873 14360184 AluSx 2224 -
-chr21 14360209 14360321 (TA)n 243 +
-chr21 14360523 14360667 L1M5 381 +
-chr21 14361271 14361298 AT_rich 27 +
-chr21 14361375 14361430 L2 215 -
-chr21 14361764 14361785 AT_rich 21 +
-chr21 14361890 14362032 MER104 355 -
-chr21 14362129 14362419 AluJo 1802 +
-chr21 14362423 14362625 MIR 528 -
-chr21 14363865 14363890 (TAA)n 204 +
-chr21 14364079 14364174 CT-rich 200 +
-chr21 14364238 14364318 (TG)n 247 +
-chr21 14365062 14365180 5S 477 +
-chr21 14365717 14368671 GSATX 1233 -
-chr21 14369544 14370155 FordPrefect 507 -
-chr21 14371111 14371192 GA-rich 315 +
-chr21 14371192 14371515 L1MC4 457 +
-chr21 14371515 14371811 AluJb 1353 +
-chr21 14371811 14371912 L1MC4 457 +
-chr21 14371912 14372205 AluSg 1930 +
-chr21 14372205 14372383 L1MC4 450 +
-chr21 14373368 14373662 AluSx 1839 +
-chr21 14373663 14373894 PABL_A 1402 +
-chr21 14373899 14373960 Alu 258 +
-chr21 14373960 14374149 AluJo 907 +
-chr21 14374282 14374591 ERVL-B4 1088 +
-chr21 14374617 14374658 AluSx 251 +
-chr21 14374658 14375237 LTR14C 4371 -
-chr21 14375237 14375500 AluSx 1698 +
-chr21 14375546 14375609 Alu 487 +
-chr21 14375666 14375697 AluSp 1022 -
-chr21 14375697 14375714 AluSp 1478 -
-chr21 14375714 14375746 (TAG)n 288 +
-chr21 14375746 14376000 AluSp 1478 -
-chr21 14376002 14376026 (TTTTG)n 183 +
-chr21 14376026 14376297 AluSg 1973 -
-chr21 14377050 14377190 AluJb 759 +
-chr21 14377207 14377252 AT_rich 31 +
-chr21 14377330 14377585 AluJb 1224 -
-chr21 14377980 14378107 LTR54B 303 +
-chr21 14378843 14379371 LSU-rRNA_Hsa 2804 -
-chr21 14379369 14379456 LSU-rRNA_Hsa 476 -
-chr21 14379456 14379759 AluSq 2183 +
-chr21 14379778 14380045 AluSx 1944 -
-chr21 14380167 14380468 AluSq 2168 -
-chr21 14381330 14381623 AluSx 1966 -
-chr21 14381974 14382256 AluSx 2079 +
-chr21 14382274 14382444 (TA)n 621 +
-chr21 14382444 14382475 AT_rich 31 +
-chr21 14382475 14382622 (TATAA)n 199 +
-chr21 14382622 14382659 AT_rich 30 +
-chr21 14382948 14382975 (GAAAA)n 201 +
-chr21 14382975 14383255 L1MEe 4304 -
-chr21 14383255 14383556 AluSx 2123 -
-chr21 14383556 14384338 L1MEe 4304 -
-chr21 14385163 14385201 AT_rich 24 +
-chr21 14385623 14385663 AT_rich 26 +
-chr21 14386207 14386260 MIR 258 +
-chr21 14386260 14387727 LTR12C 10265 -
-chr21 14387727 14387843 MIR3 258 +
-chr21 14387961 14388294 AluSx 1890 +
-chr21 14388427 14388603 AluJ 1074 -
-chr21 14388623 14388933 AluJo 1697 +
-chr21 14389102 14389123 (TAAAA)n 189 +
-chr21 14389123 14389298 FRAM 1160 +
-chr21 14389488 14389523 (T)n 195 +
-chr21 14390234 14390261 (CAAAA)n 188 +
-chr21 14390829 14390949 MER5A1 403 -
-chr21 14391092 14391190 L3 190 -
-chr21 14391272 14391404 AluJ 844 -
-chr21 14391463 14391772 AluSq 2239 -
-chr21 14392012 14392061 MIR 241 +
-chr21 14392097 14392593 (CACCAT)n 956 +
-chr21 14392599 14392753 MIR 418 -
-chr21 14392781 14392967 L3 230 -
-chr21 14394283 14394330 MIR 542 +
-chr21 14394330 14394627 AluJo 2014 +
-chr21 14394627 14394804 MIR 542 +
-chr21 14394825 14394908 MIRb 251 -
-chr21 14394940 14395230 AluSx 2134 -
-chr21 14395352 14395660 AluJb 1979 -
-chr21 14395727 14395954 MIRb 812 -
-chr21 14396579 14396864 AluSx 1968 +
-chr21 14397233 14397702 MER4A1 3253 -
-chr21 14397774 14398066 AluSq 1914 +
-chr21 14398085 14398752 L1M1 3664 -
-chr21 14398752 14399307 LTR6A 3797 +
-chr21 14399307 14399472 L1M1 3664 -
-chr21 14399611 14399915 AluSx 1809 -
-chr21 14400066 14400390 AluSg 2195 +
-chr21 14400396 14400441 (TA)n 405 +
-chr21 14400466 14400551 (TA)n 242 +
-chr21 14400935 14400966 (TG)n 279 +
-chr21 14401305 14401579 MLT1B 1918 +
-chr21 14401579 14401930 THE1D 2011 -
-chr21 14401930 14402060 MLT1B 1918 +
-chr21 14402290 14402489 MIR 496 +
-chr21 14402584 14402666 MIR 265 -
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-chr21 14404546 14405032 L1MA8 2511 -
-chr21 14405070 14405144 (TA)n 198 +
-chr21 14405145 14406037 L1MA8 5933 -
-chr21 14406037 14406259 L1PB4 975 -
-chr21 14406259 14406832 L1MA8 5933 -
-chr21 14406969 14407004 AT_rich 21 +
-chr21 14407004 14407054 L1MA8 262 -
-chr21 14407104 14407887 L1ME1 2633 +
-chr21 14407887 14408097 THE1C 1731 -
-chr21 14408097 14408385 AluSc 2078 +
-chr21 14408385 14408509 THE1C 1731 -
-chr21 14408509 14408910 HERV1_I 3203 +
-chr21 14408910 14408943 THE1C 251 -
-chr21 14408943 14409180 L1ME1 1037 +
-chr21 14409201 14409724 HERV1_LTRa 3916 +
-chr21 14409724 14418503 HERV15 35754 +
-chr21 14418503 14419001 HERV1_LTRa 3502 +
-chr21 14419001 14419036 AluSq/x 260 +
-chr21 14419036 14419197 AluJo/FRAM 841 +
-chr21 14419197 14419734 L1ME1 1168 +
-chr21 14419734 14420046 AluSc 1827 -
-chr21 14420046 14420133 L1ME1 1168 +
-chr21 14420127 14420650 L1ME1 2079 +
-chr21 14420650 14420986 MER2 1791 +
-chr21 14420986 14421184 L1ME1 2079 +
-chr21 14421990 14422192 L1M5 361 +
-chr21 14422614 14422710 MIR 194 +
-chr21 14423763 14423793 AT_rich 23 +
-chr21 14423990 14424014 AT_rich 24 +
-chr21 14424383 14424530 AluSx 945 +
-chr21 14424577 14425130 L1M2a1 5975 +
-chr21 14425130 14425407 AluY 2091 -
-chr21 14425407 14426909 L1M2a1 5975 +
-chr21 14426889 14428130 L1M2a1 9783 +
-chr21 14428130 14428443 AluJo 1445 +
-chr21 14428443 14429429 L1M2a1 9783 +
-chr21 14429432 14432281 L1M1 14762 +
-chr21 14432281 14432405 L1PB4 534 +
-chr21 14432405 14432440 L1MEe 559 +
-chr21 14432713 14432738 AT_rich 25 +
-chr21 14432790 14432811 AT_rich 21 +
-chr21 14432857 14433017 L1M5 336 -
-chr21 14433026 14433260 MIR 893 -
-chr21 14433657 14434535 L2 1523 -
-chr21 14434562 14434612 AT_rich 36 +
-chr21 14435175 14435998 HAL1b 315 -
-chr21 14436350 14436511 L1PA7 1299 +
-chr21 14436625 14436677 (TA)n 214 +
-chr21 14436677 14436975 AluJb 1801 -
-chr21 14436975 14437065 (TA)n 214 +
-chr21 14437658 14437690 AT_rich 25 +
-chr21 14439127 14439148 AT_rich 21 +
-chr21 14439419 14439610 MIRb 481 -
-chr21 14439762 14439873 GA-rich 423 +
-chr21 14440292 14440964 L2 797 +
-chr21 14440964 14441268 AluSg 2278 -
-chr21 14441268 14441694 L2 797 +
-chr21 14441707 14441854 L2 292 +
-chr21 14441853 14442155 L2 198 +
-chr21 14442281 14442516 L1ME4a 289 +
-chr21 14442614 14442967 MER7A 1684 +
-chr21 14443249 14443622 THE1C 1921 -
-chr21 14443622 14444382 THE1C-int 5208 -
-chr21 14444379 14444506 THE1D 781 -
-chr21 14446263 14446523 AluSc 1572 -
-chr21 14446586 14446666 MIR3 201 +
-chr21 14446932 14446978 (TA)n 218 +
-chr21 14447696 14448028 L1MEd 359 +
-chr21 14448297 14448319 AT_rich 22 +
-chr21 14448454 14448720 L1MEd 266 +
-chr21 14448736 14448764 AT_rich 21 +
-chr21 14449015 14449327 L1MD2 3261 +
-chr21 14449327 14449365 tRNA-Arg-AGA 243 +
-chr21 14449365 14450312 L1MD2 3261 +
-chr21 14450319 14450834 MLT1D 1768 +
-chr21 14450835 14452234 MLT1D-int 2681 +
-chr21 14452301 14452773 L1MD2 7428 +
-chr21 14452773 14452831 (TA)n 200 +
-chr21 14452831 14455453 L1MD2 7428 +
-chr21 14455505 14455667 (TA)n 316 +
-chr21 14455679 14455839 (TA)n 482 +
-chr21 14455839 14455882 AT_rich 29 +
-chr21 14455887 14456144 (TA)n 366 +
-chr21 14456147 14456236 L1MD1 435 -
-chr21 14456309 14456345 L1P5 228 +
-chr21 14456315 14456496 L1MD2 850 +
-chr21 14456500 14456839 L1MD2 1144 +
-chr21 14457228 14457270 AT_rich 28 +
-chr21 14458117 14458286 (TA)n 380 +
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-chr21 17280009 17280337 MLT1J2 524 -
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-chr21 17305015 17305067 G-rich 267 +
-chr21 17305193 17305301 MIRb 303 -
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-chr21 17307182 17307242 GA-rich 229 +
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-chr21 17309410 17309457 (AATTG)n 243 +
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-chr21 17314571 17314605 (TG)n 273 +
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-chr21 17316961 17317009 (TAA)n 411 +
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-chr21 17322369 17322824 L1MC4a 424 +
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-chr21 17323093 17323471 L1MC4a 735 +
-chr21 17323496 17324092 MLT1E2 1241 -
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-chr21 17328341 17334444 L1PA6 24053 +
-chr21 17334444 17334465 AT_rich 21 +
-chr21 17334483 17334794 AluSg 2101 -
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-chr21 17335385 17335471 FordPrefect 2994 -
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-chr21 17337523 17337551 (TC)n 252 +
-chr21 17339661 17339915 Charlie8 658 -
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-chr21 17341101 17341410 AluY 2433 -
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-chr21 17342173 17342597 MSTB1 1925 -
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-chr21 17343400 17344211 LTR27B 1304 -
-chr21 17345494 17345616 MIR3 238 -
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-chr21 17348193 17348837 L1PA16 5176 -
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-chr21 22722548 22722660 L1M4b 324 +
-chr21 22722690 22723307 L1M4b 707 +
-chr21 22723368 22723662 L1M4b 233 +
-chr21 22723778 22724149 L1ME3A 300 +
-chr21 22724231 22724405 L1ME3A 300 +
-chr21 22724936 22725269 Arthur1 433 -
-chr21 22725310 22725606 AluSc 1851 -
-chr21 22725618 22726033 L1PA16 2234 -
-chr21 22726033 22726352 AluSq 1968 -
-chr21 22726352 22726664 L1PA16 2234 -
-chr21 22726710 22726829 MIR 377 -
-chr21 22726906 22727263 LTR16A1 744 +
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-chr21 22727671 22727833 AluJb 926 +
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-chr21 22728469 22728567 LTR64 782 -
-chr21 22728567 22729121 MER41A 4037 -
-chr21 22729121 22729158 LTR64 782 -
-chr21 22729148 22729233 LTR64 382 +
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-chr21 22733650 22733946 AluSx 1994 -
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-chr21 22734100 22734264 AluSq 965 -
-chr21 22734465 22734625 FLAM_A_short_ 677 +
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-chr21 22735491 22735843 ERVL-E 594 -
-chr21 22736097 22736298 ERVL-E 471 -
-chr21 22736518 22736854 ERVL-E 297 -
-chr21 22736872 22737245 LTR40a 1018 -
-chr21 22737303 22737615 AluY 2280 -
-chr21 22737615 22737991 L1M5 738 +
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-chr21 22738137 22738173 (GA)n 183 +
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-chr21 22738584 22738669 (TA)n 534 +
-chr21 22738669 22738954 AluSq 2178 -
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-chr21 22740766 22741140 L2 242 -
-chr21 22741283 22741470 MLT1J2 388 -
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-chr21 22743031 22743438 L2 258 -
-chr21 22743529 22743646 L2 278 -
-chr21 22744349 22744410 AT_rich 40 +
-chr21 22745178 22745489 AluSq 2258 -
-chr21 22745683 22745766 CT-rich 285 +
-chr21 22745767 22746064 (TTCC)n 1284 +
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-chr21 22747910 22748072 L2 425 -
-chr21 22748072 22748110 (CA)n 248 +
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-chr21 22750553 22750724 L2 271 +
-chr21 22750810 22750832 (TA)n 198 +
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-chr21 22750976 22751344 HAL1 444 -
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-chr21 22753781 22754398 HAL1 496 +
-chr21 22754446 22754685 HAL1 472 +
-chr21 22754793 22754851 (TA)n 237 +
-chr21 22754852 22755133 AluSc 2064 -
-chr21 22755529 22755832 AluY 2471 -
-chr21 22756548 22756579 (TATATG)n 195 +
-chr21 22756583 22756879 L1PB4 3840 -
-chr21 22756879 22756907 (TTTA)n 182 +
-chr21 22756910 22757196 AluJo 1659 -
-chr21 22757196 22757721 L1PB4 3840 -
-chr21 22757721 22758097 MER1B 1860 -
-chr21 22758099 22759075 L1M3 4507 -
-chr21 22759075 22759375 AluSx 2034 -
-chr21 22759375 22759750 L1M3 4507 -
-chr21 22759779 22760000 L1M2 604 -
-chr21 22760469 22760738 AluSg 1977 +
-chr21 22761945 22762229 HAL1 375 +
-chr21 22762345 22762427 AluSg1 501 -
-chr21 22762427 22762604 AluSg/x 1091 +
-chr21 22762721 22763012 L1MDa 369 +
-chr21 22763875 22764207 L1MDa 693 +
-chr21 22764222 22764862 L1MDa 1789 +
-chr21 22764901 22765377 L1MDa 784 +
-chr21 22765370 22765685 L1MC1 4553 +
-chr21 22765685 22766056 THE1C 2673 +
-chr21 22766056 22766277 L1MC1 4553 +
-chr21 22766277 22766571 AluY 2478 +
-chr21 22766571 22767011 L1MC1 4553 +
-chr21 22767072 22767845 L1MD1 2072 +
-chr21 22767851 22767928 L2 194 +
-chr21 22768341 22768370 (CATA)n 201 +
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-chr21 22770048 22770287 MIR 689 +
-chr21 22770317 22770358 AT_rich 27 +
-chr21 22771026 22772328 L1M1 6605 +
-chr21 22772367 22772498 L1PA10 1046 +
-chr21 22772503 22774124 L1M1 7432 +
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-chr21 22774671 22774762 MLT1A 1210 +
-chr21 22774762 22775376 Tigger1 12344 +
-chr21 22775376 22775685 AluSg 2290 +
-chr21 22775685 22777413 Tigger1 12344 +
-chr21 22777413 22777642 MLT1A 1210 +
-chr21 22777642 22777671 (A)n 261 +
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-chr21 22777932 22779047 L1PA10 5838 -
-chr21 22779042 22779418 L1PA10 2676 +
-chr21 22779447 22779767 AluSg 2208 -
-chr21 22780906 22781278 L1MA4 2019 -
-chr21 22781291 22781350 Charlie9 242 -
-chr21 22781609 22781916 L1MA8 934 -
-chr21 22782939 22783033 MIRb 243 -
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-chr21 22784806 22784851 AT_rich 24 +
-chr21 22784865 22785723 L1MB3 4013 +
-chr21 22785723 22786018 AluSx 2080 +
-chr21 22786018 22786143 L1MB3 4013 +
-chr21 22786152 22786187 AluJb 589 +
-chr21 22786187 22786208 (CAAA)n 189 +
-chr21 22786208 22786340 AluJb 589 +
-chr21 22786340 22786374 (CA)n 306 +
-chr21 22786968 22786990 AT_rich 22 +
-chr21 22787164 22787214 (TATG)n 216 +
-chr21 22787257 22787299 AT_rich 21 +
-chr21 22787366 22793823 L1PA7 22258 +
-chr21 22793916 22794213 AluSc 2125 -
-chr21 22794225 22794259 AT_rich 27 +
-chr21 22794298 22794359 AT_rich 33 +
-chr21 22794438 22794752 AluJb 1669 -
-chr21 22796160 22796233 MER5B 262 +
-chr21 22798251 22798550 AluSp 2269 -
-chr21 22798568 22798606 (TTATA)n 203 +
-chr21 22798830 22799149 MLT1I 571 +
-chr21 22799232 22799325 L2 232 -
-chr21 22799599 22800025 L2 318 -
-chr21 22800325 22800358 AT_rich 26 +
-chr21 22800825 22801106 AluSx 1992 -
-chr21 22801858 22804005 L1PA16 7732 -
-chr21 22804013 22804574 L1M5 598 -
-chr21 22804574 22804597 (TTTTG)n 186 +
-chr21 22804597 22804873 L1M5 598 -
-chr21 22804873 22805177 AluSc 2193 +
-chr21 22805177 22805446 L1M5 598 -
-chr21 22805510 22805809 AluSq 2253 +
-chr21 22807248 22807302 AT_rich 40 +
-chr21 22807770 22807874 (CATATA)n 226 +
-chr21 22808137 22808449 AluJb 1839 -
-chr21 22808686 22808995 AluSg 2019 -
-chr21 22809206 22809242 AT_rich 22 +
-chr21 22809295 22809652 MER34B 777 -
-chr21 22809678 22809805 MER34C_ 271 -
-chr21 22810456 22811072 LTR77 2310 +
-chr21 22811439 22811499 AT_rich 25 +
-chr21 22812226 22812286 GA-rich 202 +
-chr21 22812441 22812732 AluSg 1782 +
-chr21 22813789 22813887 AT_rich 21 +
-chr21 22813916 22814109 AluSg 1448 -
-chr21 22814111 22815288 MER61A-int 7852 +
-chr21 22815288 22815635 MER61A 1576 +
-chr21 22815655 22815859 L1MEc 360 +
-chr21 22816145 22816770 L1M2 658 +
-chr21 22816843 22816895 L1PB4 3921 +
-chr21 22816895 22817200 AluSg 2158 +
-chr21 22817200 22817893 L1PB4 3921 +
-chr21 22817913 22818116 L1M2 380 +
-chr21 22818121 22818261 L1M2 255 +
-chr21 22818300 22818447 Tigger6 564 -
-chr21 22818448 22818553 L1MC 302 +
-chr21 22818690 22819332 Tigger6a 1856 -
-chr21 22819333 22819438 L1MC 286 +
-chr21 22819440 22819500 L1M5 324 +
-chr21 22819500 22819818 MER1B 1398 +
-chr21 22819818 22819992 L1M5 324 +
-chr21 22820004 22820134 L1MD 248 +
-chr21 22820211 22821265 L1M5 1095 +
-chr21 22821273 22821475 L1M1 590 -
-chr21 22821723 22821768 (TAA)n 229 +
-chr21 22821810 22821832 AT_rich 22 +
-chr21 22821951 22822006 AT_rich 34 +
-chr21 22822066 22824007 L1PA5 9165 -
-chr21 22823997 22824128 L1PA5 994 +
-chr21 22824678 22824990 AluSg 2218 +
-chr21 22825076 22825123 MIR 207 -
-chr21 22826096 22826496 MSTB 2072 +
-chr21 22826785 22827181 MLT1C 1569 +
-chr21 22827181 22827480 AluSg1 2079 -
-chr21 22827480 22827536 MLT1C 1569 +
-chr21 22827633 22827654 AT_rich 21 +
-chr21 22827929 22828386 L2 743 +
-chr21 22828386 22828558 L1MDa 500 +
-chr21 22828604 22829185 L1MDa 755 +
-chr21 22829176 22834382 L1PA15 14993 +
-chr21 22834382 22834678 AluY 2389 -
-chr21 22834678 22835673 L1PA15 14993 +
-chr21 22835686 22835955 L1MDa 856 +
-chr21 22835954 22836343 L1MDa 1034 +
-chr21 22836344 22836622 L1MDa 1973 +
-chr21 22836622 22837058 Tigger2a 2009 +
-chr21 22837058 22837529 L1MDa 1973 +
-chr21 22837796 22838212 MLT-int 1482 +
-chr21 22838659 22838788 L2 199 +
-chr21 22839002 22839284 AluJb 1486 +
-chr21 22839807 22839890 LOR1b 2280 +
-chr21 22839890 22840182 AluY 2395 +
-chr21 22840182 22840559 LOR1b 2280 +
-chr21 22840651 22840971 AluSx 1912 -
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-chr21 22843582 22843612 AT_rich 23 +
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-chr21 22844610 22844631 AT_rich 21 +
-chr21 22845254 22845318 L2 196 -
-chr21 22845447 22845476 AT_rich 22 +
-chr21 22845476 22845504 (TTAA)n 186 +
-chr21 22845504 22845789 AluSc 2086 -
-chr21 22845871 22845991 L1PB4 724 +
-chr21 22845990 22846111 L1MC2 488 -
-chr21 22846712 22846859 (TA)n 316 +
-chr21 22847102 22847412 AluSg 2177 -
-chr21 22847810 22847953 MER5A1 429 -
-chr21 22848019 22848057 (CA)n 267 +
-chr21 22848609 22848717 T-rich 226 +
-chr21 22849600 22849625 (T)n 225 +
-chr21 22850277 22850375 (TA)n 522 +
-chr21 22851109 22851144 AT_rich 21 +
-chr21 22851248 22851269 AT_rich 21 +
-chr21 22851608 22851723 L1MD1 296 +
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-chr21 22853008 22853179 L1P 5176 -
-chr21 22853177 22853824 L1P 5991 -
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-chr21 22854134 22854530 L1P 5991 -
-chr21 22855439 22856498 LTR28 2548 +
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-chr21 22856870 22856923 (TA)n 355 +
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-chr21 22858316 22858617 AluSc 2310 -
-chr21 22859928 22860036 MSTD 582 +
-chr21 22860038 22860210 MSTD 759 +
-chr21 22860658 22860951 AluSg 2034 -
-chr21 22860993 22861032 AT_rich 25 +
-chr21 22861878 22861929 AT_rich 37 +
-chr21 22862012 22862311 AluY 2377 -
-chr21 22862318 22862886 L1MEd 320 +
-chr21 22862936 22863069 L2 428 -
-chr21 22863119 22863614 MLT2B2 2306 -
-chr21 22863614 22863909 AluY 2509 +
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-chr21 22864161 22864241 MLT2B2 472 -
-chr21 22864391 22864453 (CAGA)n 250 +
-chr21 22864411 22864473 GA-rich 260 +
-chr21 22864781 22864905 L1MEd 254 +
-chr21 22865323 22865721 L1MEd 282 +
-chr21 22865803 22865998 L1MEd 400 +
-chr21 22866082 22866106 AT_rich 24 +
-chr21 22866113 22866420 AluSc 2158 +
-chr21 22866802 22867047 AluSq 1760 -
-chr21 22867125 22867255 L1M5 384 +
-chr21 22867450 22867472 AT_rich 22 +
-chr21 22867915 22868222 AluJb 1558 -
-chr21 22869087 22869223 L1MA1 927 -
-chr21 22869473 22869767 LTR64 907 -
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-chr21 22870111 22870132 (GAAAA)n 189 +
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-chr21 22872546 22872848 AluSg1 2309 +
-chr21 22872848 22873282 MER50 3760 +
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-chr21 22873590 22873768 MER50 3760 +
-chr21 22874411 22874713 AluSx 2051 -
-chr21 22875440 22875731 AluSg1 2106 +
-chr21 22876243 22876395 MER5A1 362 +
-chr21 22877713 22878074 L1PREC2 329 +
-chr21 22878127 22878148 AT_rich 21 +
-chr21 22878160 22878451 AluY 2279 -
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-chr21 22879629 22879665 AT_rich 22 +
-chr21 22879736 22880211 LOR1a 2876 +
-chr21 22881027 22881818 Charlie1a 3491 +
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-chr21 22884164 22884300 MER45A 573 -
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-chr21 22886885 22887181 AluSx 2113 -
-chr21 22887181 22887564 L1PB1 4540 -
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-chr21 22891734 22891821 AluSc 570 -
-chr21 22891822 22893208 LTR12C 6850 +
-chr21 22893209 22893333 LTR12D 903 +
-chr21 22893333 22893558 AluSc 1531 -
-chr21 22894135 22894184 AT_rich 35 +
-chr21 22894194 22894906 LTR8A 2843 -
-chr21 22895131 22895803 LTR8 4834 +
-chr21 22895826 22896240 MER61C 1914 -
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-chr21 22897458 22897951 L1M5 335 +
-chr21 22898162 22898532 MLT1B 1493 +
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-chr21 22899196 22899571 L3 297 +
-chr21 22899685 22899863 L1MA4A 523 +
-chr21 22899873 22899944 L1MA4A 358 +
-chr21 22899958 22899984 AT_rich 26 +
-chr21 22899995 22900569 MER4-int 12250 -
-chr21 22900569 22900888 AluSc 2104 +
-chr21 22900888 22901891 MER4-int 12250 -
-chr21 22901891 22902191 AluSx 2110 +
-chr21 22902191 22904215 MER4-int 12250 -
-chr21 22904213 22904340 MER4A1-int 784 -
-chr21 22904342 22904431 MER4A1-int 510 -
-chr21 22904427 22904801 MER4A1-int 1803 -
-chr21 22904803 22904870 MER4A1-int 516 -
-chr21 22904873 22905327 MER4A1 3210 -
-chr21 22905995 22906255 AluSc 1873 +
-chr21 22907176 22907219 AT_rich 22 +
-chr21 22907367 22907469 L3 194 -
-chr21 22907618 22907665 AT_rich 26 +
-chr21 22907999 22908244 L1PA13 1579 +
-chr21 22908533 22908978 Tigger2a 2046 -
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-chr21 22909876 22909953 MLT1H2 328 +
-chr21 22910229 22910311 L1PA6 574 -
-chr21 22910579 22910708 (TA)n 295 +
-chr21 22910717 22910888 (TTATA)n 356 +
-chr21 22910893 22910923 AT_rich 23 +
-chr21 22911857 22911998 FAM 693 +
-chr21 22911998 22912043 (CATATA)n 207 +
-chr21 22912066 22912207 MIRb 200 +
-chr21 22912334 22912813 MLT1C 1296 -
-chr21 22913076 22913098 AT_rich 22 +
-chr21 22913857 22914476 L2 1005 -
-chr21 22914478 22914523 (TG)n 203 +
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-chr21 22915291 22915607 AluSg 1780 +
-chr21 22916439 22916745 AluSg 2153 +
-chr21 22916987 22917018 (CA)n 279 +
-chr21 22917120 22917148 AT_rich 21 +
-chr21 22918103 22918450 MLT1H-int 705 +
-chr21 22918483 22918651 MLT1H 362 +
-chr21 22918675 22919034 THE1C 2182 -
-chr21 22919088 22919117 (GA)n 228 +
-chr21 22919260 22919360 MLT1H 318 +
-chr21 22920368 22920548 (TA)n 448 +
-chr21 22920637 22920739 (TA)n 294 +
-chr21 22920746 22920782 MSTC 2587 -
-chr21 22920782 22921084 AluSq 2148 +
-chr21 22921084 22921491 MSTC 2587 -
-chr21 22923388 22923470 (TA)n 355 +
-chr21 22923470 22923749 AluSp 1891 -
-chr21 22923754 22924045 AluJb 1601 -
-chr21 22924619 22924646 AT_rich 27 +
-chr21 22924819 22924846 AT_rich 27 +
-chr21 22925029 22927278 L1PA16 8027 +
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-chr21 22928378 22928504 MLT1J1 317 -
-chr21 22928504 22928554 (TCTA)n 450 +
-chr21 22928554 22928692 MLT1J2 362 -
-chr21 22929099 22929123 AT_rich 24 +
-chr21 22929264 22929299 (TGAA)n 240 +
-chr21 22929474 22929792 AluSq 2180 -
-chr21 22929934 22930197 L1MC3 1155 +
-chr21 22930521 22930545 (CAAAA)n 216 +
-chr21 22931228 22931950 L1M2 3469 -
-chr21 22931951 22933127 L1M2 2211 -
-chr21 22933125 22933505 L1MA6 9511 +
-chr21 22933505 22933547 (CA)n 378 +
-chr21 22933547 22936073 L1MA6 9511 +
-chr21 22936117 22936298 LTR16C 375 +
-chr21 22936569 22936590 (T)n 189 +
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-chr21 22938701 22938991 LTR16C 331 -
-chr21 22939696 22940130 ERVL-B4 314 -
-chr21 22940135 22940398 Tigger7 1399 +
-chr21 22940396 22940490 Tigger7 551 +
-chr21 22941325 22941350 (T)n 183 +
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-chr21 22942145 22942442 AluSg 2099 -
-chr21 22942442 22944167 L2 1484 -
-chr21 22944324 22944747 MLT1H2 600 +
-chr21 22944785 22944981 MLT1H-int 317 +
-chr21 22945096 22945254 AluJo 1184 -
-chr21 22945254 22945301 (TG)n 423 +
-chr21 22945301 22945413 AluJo 1184 -
-chr21 22945421 22945532 MLT1H-int 338 +
-chr21 22945589 22945773 MLT1H2 475 +
-chr21 22945883 22945927 (TG)n 312 +
-chr21 22945927 22946092 (TA)n 648 +
-chr21 22946148 22946187 (CA)n 330 +
-chr21 22946248 22946334 MLT1G 227 +
-chr21 22947642 22947693 Alu 245 +
-chr21 22948073 22948346 AluJo 1229 +
-chr21 22949788 22949862 MADE1 449 +
-chr21 22950561 22950597 AT_rich 29 +
-chr21 22951629 22951673 AT_rich 23 +
-chr21 22951781 22951856 L2 181 -
-chr21 22952648 22952920 L1PA4 2184 -
-chr21 22952650 22953139 L1PA4 4029 -
-chr21 22953139 22953470 L1PA4 2888 +
-chr21 22954422 22954443 AT_rich 21 +
-chr21 22955264 22955413 MIRb 242 -
-chr21 22955568 22955595 (GA)n 180 +
-chr21 22955646 22955667 AT_rich 21 +
-chr21 22955689 22955869 L1M5 429 -
-chr21 22955900 22956320 L1MD 700 +
-chr21 22956420 22956785 MSTB2 1048 -
-chr21 22956794 22957095 L1M5 333 +
-chr21 22957201 22957384 L1M5 373 +
-chr21 22957384 22957424 AT_rich 26 +
-chr21 22957446 22957934 L1M5 322 +
-chr21 22958378 22958407 AT_rich 22 +
-chr21 22959120 22959483 L1MA9 1118 +
-chr21 22960598 22960677 HAL1b 424 +
-chr21 22960677 22960962 AluSx 1929 +
-chr21 22960962 22961303 HAL1b 424 +
-chr21 22961335 22961356 AT_rich 21 +
-chr21 22961550 22961572 AT_rich 22 +
-chr21 22961652 22962032 L1MD 1037 +
-chr21 22962032 22962338 AluY 2408 +
-chr21 22962338 22962376 L1MD 1037 +
-chr21 22962393 22962694 AluY 2060 +
-chr21 22962712 22962768 Alu 271 +
-chr21 22962778 22963038 L1MC 444 +
-chr21 22963038 22963067 (GAAAA)n 219 +
-chr21 22963103 22963779 MER76 2697 +
-chr21 22963781 22964525 L1M5 2092 +
-chr21 22964534 22965092 LTR48B 1526 -
-chr21 22965102 22965264 L1M5 432 +
-chr21 22965276 22965634 THE1B 2071 +
-chr21 22965634 22967207 THE1B-int 11243 +
-chr21 22967207 22967571 THE1B 2201 +
-chr21 22967581 22967812 L1M5 522 +
-chr21 22969289 22969403 (TTCC)n 701 +
-chr21 22969404 22969495 CT-rich 370 +
-chr21 22969496 22969877 LTR16C 648 +
-chr21 22970332 22970413 MER67A 301 +
-chr21 22970413 22970899 MER67A 1813 +
-chr21 22970899 22971216 AluSx 1592 -
-chr21 22971216 22971234 MER67A 1813 +
-chr21 22971274 22971314 AT_rich 26 +
-chr21 22971476 22971919 L2 505 -
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-chr21 38351580 38352020 (TCTCTG)n 443 +
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-chr21 38650269 38650411 (CA)n 286 +
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-chr21 38659096 38659247 MER91A 236 +
-chr21 38659365 38659565 MLT1J 288 +
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-chr21 38661880 38662265 L1ME3B 756 -
-chr21 38662301 38662397 MSTA 699 -
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-chr21 43089506 43089757 MER83C 1573 -
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-chr21 43128140 43128368 FordPrefect 493 +
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-chr21 43129336 43129415 L1MC4a 2603 -
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-chr21 43133369 43133521 (TG)n 270 +
-chr21 43133577 43133752 (TG)n 454 +
-chr21 43133770 43133993 (TG)n 484 +
-chr21 43134008 43134183 (TG)n 466 +
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-chr21 43135806 43136342 L1ME3A 353 +
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-chr21 43136756 43137037 AluSg 1912 -
-chr21 43137037 43137159 AluJo 1886 -
-chr21 43137183 43137554 L1ME3A 275 +
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-chr21 43139327 43139541 L1ME3A 962 +
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-chr21 43415181 43415605 LTR49-int 2298 -
-chr21 43415605 43415902 AluJb 1660 +
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-chr21 43416268 43416330 LTR49-int 2298 -
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-chr21 43417368 43417521 AluSg/x 1129 +
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-chr21 43418108 43419084 MER57A-int 5999 +
-chr21 43419084 43419385 AluSq 2457 -
-chr21 43419385 43419577 LTR23-int 2676 +
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-chr21 43419986 43420021 (TTTA)n 294 +
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-chr21 43420352 43420498 LTR23-int 2676 +
-chr21 43420505 43420584 LTR23 504 +
-chr21 43420604 43420819 AluJb 1286 +
-chr21 43420822 43420951 LTR24 582 +
-chr21 43420953 43421205 (TCCA)n 791 +
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-chr21 43422710 43422964 Tigger4(Zombi) 259 +
-chr21 43422964 43423264 AluJb 1977 +
-chr21 43423264 43423296 Tigger4(Zombi) 259 +
-chr21 43423476 43423653 Tigger4(Zombi) 476 +
-chr21 43423831 43424297 MER4A1 3327 -
-chr21 43424870 43425129 LTR24B 2366 -
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-chr21 43425441 43425581 LTR24B 2366 -
-chr21 43425581 43425622 AluJ/FLAM 465 +
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-chr21 43432750 43433035 AluSp 2218 +
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-chr21 43436173 43436211 THE1D 2034 +
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-chr21 43437857 43437894 THE1A 1799 +
-chr21 43437894 43438199 AluSq 2374 -
-chr21 43438199 43438490 THE1A 1799 +
-chr21 43438490 43438629 AluJb 804 -
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-chr21 43439822 43440214 L1MB3 1521 +
-chr21 43440308 43441268 LTR5_Hs 8793 -
-chr21 43441754 43442055 AluJo 1987 +
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-chr21 43443345 43443504 AluSx 1896 +
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-chr21 43450246 43450268 L1M5 409 +
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-chr21 43530092 43530197 MLT1B 545 +
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-chr21 43580237 43580757 (CCA)n 1197 +
-chr21 43580762 43580848 (CACCAT)n 1012 +
-chr21 43580848 43581027 (CCA)n 1209 +
-chr21 43581027 43581117 (CACCAT)n 1012 +
-chr21 43581135 43581382 (CCA)n 1221 +
-chr21 43581382 43581562 (CACCAT)n 1023 +
-chr21 43581562 43581953 (CCA)n 1161 +
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-chr21 43584152 43584378 MLT1D 634 +
-chr21 43586638 43586981 (CA)n 861 +
-chr21 43589227 43589362 MIR3 286 +
-chr21 43589449 43589554 MER63D 426 +
-chr21 43592305 43592506 MER58 567 -
-chr21 43593962 43594060 MIR 186 -
-chr21 43594418 43594487 C-rich 223 +
-chr21 43594850 43594937 MER81 400 -
-chr21 43595445 43595610 L1ME4a 435 -
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-chr21 43595694 43596069 MER74B 1210 +
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-chr21 46870189 46870298 MLT1F-int 508 +
-chr21 46870299 46870846 MLT1G1-int 1143 -
-chr21 46870861 46871020 MLT1H-int 281 -
-chr21 46871026 46871493 MLT1G 703 -
-chr21 46871541 46871918 THE1C 2596 -
-chr21 46871919 46872007 MLT1B 1669 +
-chr21 46872007 46872430 LTR47A 2432 -
-chr21 46872430 46872737 MLT1B 1669 +
-chr21 46872785 46873070 MLT1E 904 -
-chr21 46873095 46873454 LTR52 646 +
-chr21 46873520 46874124 L1MEc 858 -
-chr21 46874124 46874428 AluSx 1964 +
-chr21 46874428 46874507 L1MEc 858 -
-chr21 46874507 46874602 L1PA7 709 -
-chr21 46874602 46874919 L1MEc 295 -
-chr21 46874934 46875153 L1MEc 313 -
-chr21 46875147 46875975 L1PA7 6504 -
-chr21 46875951 46876130 L1P2 946 -
-chr21 46876132 46877492 MER4-int 9929 -
-chr21 46877492 46877787 AluSx 1871 +
-chr21 46877787 46878473 MER4-int 9929 -
-chr21 46878473 46878547 L4 180 -
-chr21 46878547 46878778 MER4-int 9929 -
-chr21 46878781 46879238 MER4A1 3169 -
-chr21 46879243 46879427 MER4B 623 -
-chr21 46879943 46879972 GC_rich 22 +
-chr21 46881993 46882135 L1MCa 337 +
-chr21 46882163 46882318 FAM 866 +
-chr21 46882338 46882630 L1ME3B 441 -
-chr21 46882709 46883022 L1M5 489 -
-chr21 46883100 46884029 L1MEc 2905 -
-chr21 46884029 46884067 (TG)n 309 +
-chr21 46884067 46884748 L1MEc 2905 -
-chr21 46884778 46885039 AluY 1999 -
-chr21 46885048 46885259 L1M4 307 -
-chr21 46885340 46885480 AluJb 878 +
-chr21 46885502 46885745 L1MC4a 301 +
-chr21 46885745 46886054 AluSx 1935 +
-chr21 46886059 46886096 (TG)n 270 +
-chr21 46886242 46886708 L1ME4a 405 +
-chr21 46886812 46886962 L1ME4a 361 +
-chr21 46887080 46887388 AluSx 1967 +
-chr21 46888920 46889201 MER58B 1178 -
-chr21 46889293 46889629 AluJo 1519 +
-chr21 46889638 46889821 AluJo 850 +
-chr21 46889914 46890044 L1ME3B 405 +
-chr21 46890044 46890353 AluSx 1946 -
-chr21 46890353 46890614 L1ME3B 405 +
-chr21 46890829 46891136 L1MC4a 413 -
-chr21 46891141 46891421 MLT1A1 693 -
-chr21 46891477 46891642 L1MC4_3endX 343 -
-chr21 46891836 46892003 FRAM 650 -
-chr21 46892029 46892086 AT_rich 22 +
-chr21 46892396 46892604 L1MC4a 314 -
-chr21 46892583 46892681 L1MD 293 -
-chr21 46896438 46896576 L1PREC2 277 +
-chr21 46896932 46897040 L1ME4a 288 +
-chr21 46898261 46898291 (T)n 195 +
-chr21 46898475 46898726 L1ME4a 442 +
-chr21 46898714 46898903 L1MD2 776 +
-chr21 46898903 46899208 MER2 1135 +
-chr21 46899304 46899922 L1MD2 2612 +
-chr21 46899916 46900310 L1MD2 1306 +
-chr21 46900317 46900724 MSTB1 2258 +
-chr21 46900724 46902105 L1MD2 2718 +
-chr21 46902161 46902336 L1ME4a 384 +
-chr21 46902470 46902579 MER45B 546 -
-chr21 46903800 46903973 L1M5 344 +
-chr21 46904289 46904311 AT_rich 22 +
-chr21 46906284 46906449 G-rich 373 +
-chr21 46909243 46909287 L2 195 +
-chr21 46909413 46909464 AT_rich 23 +
-chr21 46909464 46909768 AluJo 2015 +
-chr21 46909769 46910593 L1ME3A 1283 -
-chr21 46910643 46910947 AluSx 2427 -
-chr21 46911036 46911163 AluJo 773 +
-chr21 46911163 46911432 AluSx 2091 +
-chr21 46913108 46913727 L1PA3 5539 -
-chr21 46915754 46916276 MLT1E2 1609 -
-chr21 46916330 46916418 L1M5 226 -
-chr21 46916433 46916857 L1M5 1626 -
-chr21 46916857 46917170 AluJo 1400 +
-chr21 46917170 46917283 L1M5 1626 -
-chr21 46917286 46917758 L1MA4A 2227 +
-chr21 46917764 46917862 L1MA4A 435 +
-chr21 46917957 46918166 MIR 320 -
-chr21 46918500 46918536 AT_rich 22 +
-chr21 46918925 46919030 GA-rich 252 +
-chr21 46919402 46919654 L2 390 +
-chr21 46919654 46919928 AluSx 1723 -
-chr21 46919928 46920171 L2 390 +
-chr21 46920752 46922048 L1PA7 7374 -
-chr21 46922123 46922411 L1ME1 883 +
-chr21 46922411 46922704 AluJb 1385 -
-chr21 46922718 46922935 L1ME1 699 +
-chr21 46923377 46923802 MLT1K 323 -
-chr21 46924116 46924575 HAL1 655 +
-chr21 46924661 46924875 MER74A 443 +
-chr21 46925595 46925624 AT_rich 22 +
-chr21 46926764 46927048 MLT1I 641 -
-chr21 46927048 46927090 (A)n 378 +
-chr21 46927155 46927194 MLT1I 248 -
-chr21 46927433 46927614 (TTAGGG)n 234 +
-chr21 46928301 46928745 MER4A1 2938 -
-chr21 46929613 46930969 L1MC3 5007 -
-chr21 46930969 46931413 MSTB1 1749 -
-chr21 46931413 46931818 L1MC3 5007 -
-chr21 46931945 46932055 MER34B-int 303 -
-chr21 46932058 46932281 AluJb 1504 -
-chr21 46932282 46932323 AluJb 228 -
-chr21 46932323 46932751 MER34B-int 2060 -
-chr21 46932771 46933151 LTR10C 1336 -
-chr21 46933171 46933204 (CA)n 297 +
-chr21 46933260 46934052 MER34B-int 3116 -
-chr21 46934052 46934352 AluY 2333 -
-chr21 46934352 46934522 MER34B-int 3116 -
-chr21 46934536 46935047 MER34B-int 1297 -
-chr21 46935651 46936098 MER34B-int 1588 -
-chr21 46936101 46936169 MLT2B3 330 +
-chr21 46936194 46936262 MLT2B3 406 +
-chr21 46936287 46936355 MLT2B3 375 +
-chr21 46936380 46936448 MLT2B3 330 +
-chr21 46936473 46936541 MLT2B3 346 +
-chr21 46936566 46936632 MLT2B3 335 +
-chr21 46936657 46936725 MLT2B5 417 +
-chr21 46936750 46936977 MLT2B3 2194 +
-chr21 46936977 46937339 THE1C 2217 +
-chr21 46937339 46937689 MLT2B5 1691 +
-chr21 46937696 46938061 MER34B-int 678 -
-chr21 46938036 46938374 MER34B-int 910 -
-chr21 46938415 46938527 MER34B-int 268 -
-chr21 46938776 46938841 MER72 3923 -
-chr21 46938841 46939137 AluSq 2287 -
-chr21 46939137 46939777 MER72 3923 -
-chr21 46939986 46940174 L1MC 565 -
-chr21 46940179 46940735 MER34C_ 2769 -
-chr21 46940746 46941357 L1MC 1506 -
-chr21 46941373 46941479 LTR60 529 +
-chr21 46941590 46941894 AluYb8 2829 +
-chr21 46941894 46942298 LTR60 958 +
-chr21 46942142 46944181 TAR1 16459 +
-chr21 46944181 46944323 (TTAGGG)n 1057 +
diff --git a/data/simpleRepeats.chr1.bed.gz b/data/simpleRepeats.chr1.bed.gz
new file mode 100644
index 0000000..6beb270
Binary files /dev/null and b/data/simpleRepeats.chr1.bed.gz differ
diff --git a/docs/_static/labibi.css b/docs/_static/labibi.css
new file mode 100644
index 0000000..649caef
--- /dev/null
+++ b/docs/_static/labibi.css
@@ -0,0 +1,54 @@
+ at import url('rtd.css');
+
+/* Styles for floating Edit on GitHub box */
+#editor-trap {
+ margin: 1em;
+ padding: 1em;
+ border: 1px solid black;
+ box-shadow: 0 0 3px black;
+ width: 200px;
+
+ background: #fefabc;
+ position: fixed;
+ bottom: 4em;
+ left: 1em;
+ font-size: 60%;
+ text-align: left;
+ z-index: 2;
+
+ -moz-transform: rotate(-4deg);
+ -webkit-transform: rotate(-4deg);
+ -o-transform: rotate(-4deg);
+ -ms-transform: rotate(-4deg);
+ transform: rotate(-4deg);
+ box-shadow: 0px 4px 6px #333;
+ -moz-box-shadow: 0px 4px 6px #333;
+ -webkit-box-shadow: 0px 4px 6px #333;
+
+
+ cursor: pointer;
+}
+
+#editor-trap h3 {
+ margin: 0 0 0.5em 0;
+ padding: 0;
+ background: transparent;
+}
+
+#editor-trap ol {
+ margin: 0;
+ padding: 0 0 0 2em;
+}
+
+/* Hide trick */
+
+#editor-trap.toggled > * {
+ display: none;
+}
+
+
+#editor-trap.toggled > h3 {
+ display: block;
+}
+
+
diff --git a/docs/_static/labibi.js b/docs/_static/labibi.js
new file mode 100644
index 0000000..e548131
--- /dev/null
+++ b/docs/_static/labibi.js
@@ -0,0 +1,30 @@
+// Store editor pop-up help state in localStorage
+// so it does not re-pop-up itself between page loads.
+// Do not even to pretend to support IE gracefully.
+(function($) {
+
+ $(document).ready(function() {
+ var box = $("#editor-trap");
+ var klass = "toggled";
+ var storageKey = "toggled";
+
+ function toggle() {
+ box.toggleClass(klass);
+ // Store the toggle status in local storage as "has value string" or null
+ window.localStorage.setItem(storageKey, box.hasClass(klass) ? "toggled" : "not-toggled");
+ }
+
+ box.click(toggle);
+
+ // Check the persistent state of the editor pop-up
+ // Note that localStorage does not necessarily support boolean values (ugh!)
+ // http://stackoverflow.com/questions/3263161/cannot-set-boolean-values-in-localstorage
+ var v = window.localStorage.getItem(storageKey);
+ if(v == "toggled" || !v) {
+ box.addClass(klass);
+ }
+
+ });
+
+})(jQuery);
+
diff --git a/docs/bedtools.ai b/docs/bedtools.ai
index c962cbd..0d4d023 100644
--- a/docs/bedtools.ai
+++ b/docs/bedtools.ai
@@ -1,5 +1,5 @@
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<xmp:CreateDate>2012-07-21T10:47:59-04:00</xmp:CreateDate>
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- <xmp:MetadataDate>2012-07-21T10:55:26-04:00</xmp:MetadataDate>
+ <xmp:ModifyDate>2013-03-11T10:09:58-04:00</xmp:ModifyDate>
+ <xmp:MetadataDate>2013-03-11T10:09:58-04:00</xmp:MetadataDate>
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+ <xmpMM:InstanceID>uuid:5c3abbd9-12ad-0844-ae18-e628adb0a70b</xmpMM:InstanceID>
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+ <stFnt:fontFamily>CMU Serif</stFnt:fontFamily>
+ <stFnt:fontFace>Roman</stFnt:fontFace>
+ <stFnt:fontType>Open Type</stFnt:fontType>
+ <stFnt:versionString>Version 0.7.0 </stFnt:versionString>
+ <stFnt:composite>False</stFnt:composite>
+ <stFnt:fontFileName>cmunrm.otf</stFnt:fontFileName>
+ </rdf:li>
+ <rdf:li rdf:parseType="Resource">
<stFnt:fontName>CapitalsRegular</stFnt:fontName>
<stFnt:fontFamily>Capitals</stFnt:fontFamily>
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@@ -212,15 +221,6 @@
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\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 0d30336..f5c2ebf 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -28,7 +28,7 @@ extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
'sphinx.ext.intersphinx', 'sphinx.ext.todo',
'sphinx.ext.coverage', 'sphinx.ext.pngmath',
'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
- 'matplotlib.sphinxext.plot_directive']
+ 'matplotlib.sphinxext.plot_directive']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']
@@ -44,16 +44,16 @@ master_doc = 'index'
# General information about the project.
project = u'bedtools'
-copyright = u'2012'
+copyright = u'2009 - 2013, Aaron R. Quinlan'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
-version = '2.16.2'
+version = '2.19.0'
# The full version, including alpha/beta/rc tags.
-release = '2.16.2'
+release = '2.19.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -123,7 +123,8 @@ html_favicon = 'bedtools.png'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+html_static_path = ['_static']
+html_style = 'labibi.css'
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
@@ -134,7 +135,9 @@ html_last_updated_fmt = '%b %d, %Y'
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+html_sidebars = {
+ 'index': ['sidebar-intro.html', 'sourcelink.html', 'searchbox.html']
+}
# Additional templates that should be rendered to pages, maps page names to
# template names.
@@ -220,7 +223,7 @@ man_pages = [
]
# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}
class Mock(object):
def __init__(self, *args, **kwargs):
diff --git a/docs/content/advanced-usage.rst b/docs/content/advanced-usage.rst
index 8f70680..476f3a9 100755
--- a/docs/content/advanced-usage.rst
+++ b/docs/content/advanced-usage.rst
@@ -4,89 +4,98 @@ Advanced usage
==========================================================================
-7.1 Mask all regions in a genome except for targeted capture regions.
+Mask all regions in a genome except for targeted capture regions.
==========================================================================
-# Add 500 bp up and downstream of each probe
-::
- slopBed -i probes.bed -b 500 > probes.500bp.bed
+
+Step 1. Add 500 bp up and downstream of each probe
+
+.. code-block:: bash
+
+ bedtools slop -i probes.bed -b 500 > probes.500bp.bed
-# Get a BED file of all regions not covered by the probes (+500 bp up/down)
-::
- complementBed -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
+Step 2. Get a BED file of all regions not covered by the probes (+500 bp up/down)
+
+.. code-block:: bash
+
+ bedtools complement -i probes.500bp.bed -g hg18.genome > probes.500bp.complement.bed
-# Create a masked genome where all bases are masked except for the probes +500bp
-::
- maskFastaFromBed -in hg18.fa -bed probes.500bp.complement.bed -fo hg18.probecomplement.
- masked.fa
+
+Step 3. Create a masked genome where all bases are masked except for the probes +500bp
+
+.. code-block:: bash
+
+ bedtools maskfasta -in hg18.fa -bed probes.500bp.complement.bed -fo \
+ > hg18.probecomplement.masked.fa
==========================================================================
-7.2 Screening for novel SNPs.
+Screening for novel SNPs.
==========================================================================
-# Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
-::
- intersectBed -a snp.calls.bed -b dbSnp.bed -v | intersectBed -a stdin -b 1KG.bed
- -v > snp.calls.novel.bed
+Find all SNPs that are not in dbSnp and not in the latest 1000 genomes calls
+
+.. code-block:: bash
+ bedtools intersect -a snp.calls.bed -b dbSnp.bed -v | \
+ bedtools intersect -a - -b 1KG.bed -v | \
+ > snp.calls.novel.bed
==========================================================================
-7.3 Computing the coverage of features that align entirely within an
-interval.
+Computing the coverage of features that align entirely within an interval.
==========================================================================
-# By default, coverageBed counts any feature in A that overlaps B by >= 1 bp. If
-you want to require that a feature align entirely within B for it to be counted,
-you can first use intersectBed with the "-f 1.0" option.
-::
- intersectBed -a features.bed -b windows.bed -f 1.0 | coverageBed -a stdin -b
- windows.bed > windows.bed.coverage
+
+By default, bedtools ``coverage`` counts any feature in A that overlaps B
+by >= 1 bp. If you want to require that a feature align entirely within B for
+it to be counted, you can first use intersectBed with the "-f 1.0" option.
+
+.. code-block:: bash
+
+ bedtools intersect -a features.bed -b windows.bed -f 1.0 | \
+ bedtools coverage -a - -b windows.bed \
+ > windows.bed.coverage
==========================================================================
-7.4 Computing the coverage of BAM alignments on exons.
+Computing the coverage of BAM alignments on exons.
==========================================================================
-# One can combine SAMtools with BEDtools to compute coverage directly from the BAM
-data by using bamToBed.
-::
- bamToBed -i reads.bam | coverageBed -a stdin -b exons.bed > exons.bed.coverage
+One can combine ``samtools`` with ``bedtools`` to compute coverage directly
+from the BAM data by using ``bamtobed``.
+
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam | \
+ bedtools coverage -a - -b exons.bed \
+ > exons.bed.coverage
-# Take it a step further and require that coverage be from properly-paired reads.
-::
- samtools view -bf 0x2 reads.bam | bamToBed -i stdin | coverageBed -a stdin -b
- exons.bed > exons.bed.proper.coverage
+Take it a step further and require that coverage be from properly-paired reads.
+.. code-block:: bash
-==========================================================================
-7.5 Computing coverage separately for each strand.
-==========================================================================
-# Use grep to only look at forward strand features (i.e. those that end in "+").
-::
- bamToBed -i reads.bam | grep \+$ | coverageBed -a stdin -b genes.bed >
- genes.bed.forward.coverage
+ samtools view -uf 0x2 reads.bam | \
+ coverageBed -abam - -b exons.bed \
+ > exons.bed.proper.coverage
-# Use grep to only look at reverse strand features (i.e. those that end in "-").
-::
- bamToBed -i reads.bam | grep \-$ | coverageBed -a stdin -b genes.bed >
- genes.bed.forward.coverage
-
==========================================================================
-7.6 Find structural variant calls that are private to one sample.
+Computing coverage separately for each strand.
==========================================================================
-# :
-::
- pairToPair -a sample1.sv.bedpe -b othersamples.sv.bedpe -type neither >
- sample1.sv.private.bedpe
-
-
+Use grep to only look at forward strand features (i.e. those that end in "+").
+
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam | \
+ grep \+$ | \
+ bedtools coverage -a - -b genes.bed \
+ > genes.bed.forward.coverage
+
+Use grep to only look at reverse strand features (i.e. those that end in "-").
+
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam | \
+ grep \-$ | \
+ bedtools coverage -a - -b genes.bed \
+ > genes.bed.reverse.coverage
-==================================================================================
-7.7 Exclude SV deletions that appear to be ALU insertions in the reference genome.
-==================================================================================
-# We'll require that 90% of the inner span of the deletion be overlapped by a
-recent ALU.
-::
- pairToBed -a deletions.sv.bedpe -b ALUs.recent.bed -type notispan -f 0.80 >
- deletions.notALUsinRef.bedpe
\ No newline at end of file
diff --git a/docs/content/annotateBed.rst b/docs/content/annotateBed.rst
deleted file mode 100755
index 9a55b3b..0000000
--- a/docs/content/annotateBed.rst
+++ /dev/null
@@ -1,99 +0,0 @@
-###############
-5.24 annotateBed
-###############
-**annotateBed** annotates one BED/VCF/GFF file with the coverage and number of overlaps observed
-from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature
-coincides with multiple other feature types with a single command.
-
-==========================================================================
-5.24.1 Usage and option summary
-==========================================================================
-Usage:
-::
- annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
-
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-
-=========================== ===============================================================================================================================================================================================================
-**-namesr** A list of names (one per file) to describe each file in -i. These names will be printed as a header line.
-**-counts** Report the count of features in each file that overlap -i. Default behavior is to report the fraction of -i covered by each file.
-**-both** Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file.
-**-s** Force strandedness. That is, only include hits in A that overlap B on the same strand. By default, hits are included without respect to strand.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-==========================================================================
-5.24.2 Default behavior - annotate one file with coverage from others.
-==========================================================================
-By default, the fraction of each feature covered by each annotation file is reported after the complete
-feature in the file to be annotated.
-::
- cat variants.bed
- chr1 100 200 nasty 1 -
- chr2 500 1000 ugly 2 +
- chr3 1000 5000 big 3 -
-
- cat genes.bed
- chr1 150 200 geneA 1 +
- chr1 175 250 geneB 2 +
- chr3 0 10000 geneC 3 -
-
- cat conserve.bed
- chr1 0 10000 cons1 1 +
- chr2 700 10000 cons2 2 -
- chr3 4000 10000 cons3 3 +
-
- cat known_var.bed
- chr1 0 120 known1 -
- chr1 150 160 known2 -
- chr2 0 10000 known3 +
-
- annotateBed -i variants.bed -files genes.bed conserv.bed known_var.bed
- chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
- chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
- chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000
-
-
-==========================================================================
-5.24.3 Report the count of hits from the annotation files
-==========================================================================
-Figure:
-::
- annotateBed -counts -i variants.bed -files genes.bed conserv.bed known_var.bed
- chr1 100 200 nasty 1 - 2 1 2
- chr2 500 1000 ugly 2 + 0 1 1
- chr3 1000 5000 big 3 - 1 1 0
-
-
-
-==========================================================================
-5.24.4 Report both the count of hits and the fraction covered from the annotation files
-==========================================================================
-Figure:
-::
- annotateBed -both -i variants.bed -files genes.bed conserv.bed known_var.bed
- #chr start end name score +/- cnt1 pct1 cnt2 pct2 cnt3 pct3
- chr1 100 200 nasty 1 - 2 0.500000 1 1.000000 2 0.300000
- chr2 500 1000 ugly 2 + 0 0.000000 1 0.600000 1 1.000000
- chr3 1000 5000 big 3 - 1 1.000000 1 0.250000 0 0.000000
-
-
-
-
-==========================================================================
-5.24.5 Restrict the reporting to overlaps on the same strand.
-==========================================================================
-Note: Compare with the result from 5.24.3
-::
- annotateBed -s -i variants.bed -files genes.bed conserv.bed known_var.bed
- chr1 100 200 nasty var1 - 0.000000 0.000000 0.000000
- chr2 500 1000 ugly var2 + 0.000000 0.000000 0.000000
- chr3 1000 5000 big var3 - 1.000000 0.000000 0.000000
-
-
-
diff --git a/docs/content/bamToBed.rst b/docs/content/bamToBed.rst
deleted file mode 100755
index 8647e92..0000000
--- a/docs/content/bamToBed.rst
+++ /dev/null
@@ -1,88 +0,0 @@
-###############
-5.4 bamToBed
-###############
-
-**bamToBed** is a general purpose tool that will convert sequence alignments in BAM format to either
-BED6, BED12 or BEDPE format. This enables one to convert BAM files for use with all of the other
-BEDTools. The CIGAR string is used to compute the alignment end coordinate in an "ungapped"
-fashion. That is, match ("M"), deletion ("D"), and splice ("N") operations are observed when computing
-alignment ends.
-
-============================================
-5.4.1 Usage and option summary
-============================================
-**Usage:**
-::
- bamToBed [OPTIONS] -i <BAM>
-
-
-====================== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
-Option Description
-====================== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
-**-bedpe** Write BAM alignments in BEDPE format. Only one alignment from paired-end reads will be reported. Specifically, it each mate is aligned to the same chromosome, the BAM alignment reported will be the one where the BAM insert size is greater than zero. When the mate alignments are interchromosomal, the lexicographically lower chromosome will be reported first. Lastly, when an end is unmapped, the chromosome and strand will be set to "." and the start and end coordinat [...]
- **NOTE: When using this option, it is required that the BAM file is sorted/grouped by the read name. This allows bamToBed to extract correct alignment coordinates for each end based on their respective CIGAR strings. It also assumes that the alignments for a given pair come in groups of twos. There is not yet a standard method for reporting multiple alignments using BAM. bamToBed will fail if an aligner does not report alignments in pairs**.
- BAM files may be piped to bamToBed by specifying "-i stdin". See example below.
-**-bed12** Write "blocked" BED (a.k.a. BED12) format. This will convert "spliced" BAM alignments (denoted by the "N" CIGAR operation) to BED12.
-**-ed** Use the "edit distance" tag (NM) for the BED score field. Default for BED is to use mapping quality. Default for BEDPE is to use the *minimum* of the two mapping qualities for the pair. When -ed is used with -bedpe, the total edit distance from the two mates is reported.
-**-tag** Use other *numeric* BAM alignment tag for BED score. Default for BED is to use mapping quality. Disallowed with BEDPE output.
-**-color** An R,G,B string for the color used with BED12 format. Default is (255,0,0).
-**-split** Report each portion of a "split" BAM (i.e., having an "N" CIGAR operation) alignment as a distinct BED intervals.
-====================== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
-
-By default, each alignment in the BAM file is converted to a 6 column BED. The BED "name" field is
-comprised of the RNAME field in the BAM alignment. If mate information is available, the mate (e.g.,
-"/1" or "/2") field will be appended to the name. The "score" field is the mapping quality score from the
-BAM alignment, unless the **-ed** option is used.
-
-Examples:
-::
- bamToBed -i reads.bam | head -5
- chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 37 -
- chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 37 +
- chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 37 -
-
- bamToBed -i reads.bam -tag NM | head -5
- chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 1 -
- chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 3 +
- chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 1 -
-
- bamToBed -i reads.bam -bedpe | head -3
- chr7 118965072 118965122 chr7 118970079 118970129
- TUPAC_0001:3:1:0:1452#0 37 + -
- chr11 46765606 46765656 chr11 46769934 46769984
- TUPAC_0001:3:1:0:1472#0 37 + -
- chr20 54704674 54704724 chr20 54708987 54709037
- TUPAC_0001:3:1:1:1833#0 37 +
-
-
-One can easily use samtools and bamToBed together as part of a UNIX pipe. In this example, we will
-only convert properly-paired (BAM flag == 0x2) reads to BED format.
-::
- samtools view -bf 0x2 reads.bam | bamToBed -i stdin | head
- chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 37 -
- chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 37 +
- chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 37 -
- chr11 46765606 46765656 TUPAC_0001:3:1:0:1472#0/2 37 +
- chr20 54704674 54704724 TUPAC_0001:3:1:1:1833#0/1 37 +
- chr20 54708987 54709037 TUPAC_0001:3:1:1:1833#0/2 37 -
- chrX 9380413 9380463 TUPAC_0001:3:1:1:285#0/1 0 -
- chrX 9375861 9375911 TUPAC_0001:3:1:1:285#0/2 0 +
- chrX 131756978 131757028 TUPAC_0001:3:1:2:523#0/1 37 +
- chrX 131761790 131761840 TUPAC_0001:3:1:2:523#0/2 37 -
-
-
-==================================================================
-5.4.2 (-split)Creating BED12 features from "spliced" BAM entries.
-==================================================================
-bamToBed will, by default, create a BED6 feature that represents the entire span of a spliced/split
-BAM alignment. However, when using the **-split** command, a BED12 feature is reported where BED
-blocks will be created for each aligned portion of the sequencing read.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Exons *************** **********
-
- BED/BAM A ^^^^^^^^^^^^....................................^^^^
-
- Result =============== ====
-
diff --git a/docs/content/bedToIgv.rst b/docs/content/bedToIgv.rst
deleted file mode 100755
index 64d7578..0000000
--- a/docs/content/bedToIgv.rst
+++ /dev/null
@@ -1,68 +0,0 @@
-###############
-5.20 bedToIgv
-###############
-**bedToIgv** creates an IGV (http://www.broadinstitute.org/igv/) batch script (see: http://
-www.broadinstitute.org/igv/batch for details) such that a ��snapshot�� will be taken at each features in a
-feature file. This is useful as an efficient means for quickly collecting images of primary data at several
-loci for subsequent screening, etc.
-
-**NOTE: One must use IGV version 1.5 or higher.**
-
-
-
-==========================================================================
-5.20.1 Usage and option summary
-==========================================================================
-Usage:
-::
- bedToIgv [OPTIONS] -i <BED/GFF/VCF> > <igv.batch>
-
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-path** The full path to which the IGV snapshots should be written. *Default: ./*
-**-sess** The full path to an existing IGV session file to be loaded prior to taking snapshots. *Default is for no session to be loaded and the assumption is that you already have IGV open and loaded with your relevant data prior to running the batch script*.
-**-sort** The type of BAM sorting you would like to apply to each image. **Valid sorting options**: *base, position, strand, quality, sample, and readGroup Default is to apply no sorting at all*.
-**-clps** Collapse the aligned reads prior to taking a snapshot. *Default is to not collapse*.
-**-name** Use the "name" field (column 4) for each image's filename. *Default is to use the "chr:start-pos.ext"*.
-**-slop** Number of flanking base pairs on the left & right of the image.
-**-img** The type of image to be created. **Valid options**: *png, eps, svg Default is png*.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-==========================================================================
-5.20.2 Default behavior
-==========================================================================
-Figure:
-::
- bedToIgv -i data/rmsk.hg18.chr21.bed | head -9
- snapshotDirectory ./
- goto chr21:9719768-9721892
- snapshot chr21:9719768-9721892.png
- goto chr21:9721905-9725582
- snapshot chr21:9721905-9725582.png
- goto chr21:9725582-9725977
- snapshot chr21:9725582-9725977.png
- goto chr21:9726021-9729309
- snapshot chr21:9726021-9729309.png
-
-
-
-
-==========================================================================
-5.20.3 Using a bedToIgv batch script within IGV.
-==========================================================================
-Once an IGV batch script has been created with **bedToIgv**, it is simply a matter of running it from
-within IGV.
-
-For example, first create the batch script:
-::
- bedToIgv -i data/rmsk.hg18.chr21.bed > rmsk.igv.batch
-
-Then, open and launch the batch script from within IGV. This will immediately cause IGV to begin
-taking snapshots of your requested regions.
-
diff --git a/docs/content/bedtools-suite.rst b/docs/content/bedtools-suite.rst
index bbe1802..936d8ad 100755
--- a/docs/content/bedtools-suite.rst
+++ b/docs/content/bedtools-suite.rst
@@ -1,45 +1,59 @@
-###############
+##################
The BEDTools suite
-###############
+##################
-This section covers the functionality and default / optional usage for each of the available BEDTools.
-Example "figures" are provided in some cases in an effort to convey the purpose of the tool. The
-behavior of each available parameter is discussed for each tool in abstract terms. More concrete usage
-examples are provided in **Section 6**.
+`bedtools` consists of a suite of sub-commands that are invoked as follows::
+ bedtools [sub-command] [options]
-=================
-Table of contents
-=================
+For example, to intersect two BED files, one would invoke the following::
+
+ bedtools intersect -a a.bed -b b.bed
+
+=========================================
+The full list of `bedtools` sub-commands.
+=========================================
.. toctree::
:maxdepth: 1
- intersectBed
- pairToBed
- pairToPair
- bamToBed
- windowBed
- closestBed
- subtractBed
- mergeBed
- coverageBed
- genomecoverageBed
- fastafromBed
- maskfastafromBed
- shuffleBed
- slopBed
- sortBed
- linksBed
- complementBed
- bedToBam
- overlap
- bedToIgv
- bed12ToBed6
- groupBy
- unionBedGraphs
- annotateBed
-
-
+ tools/annotate
+ tools/bamtobed
+ tools/bamtofastq
+ tools/bed12tobed6
+ tools/bedpetobam
+ tools/bedtobam
+ tools/closest
+ tools/cluster
+ tools/complement
+ tools/coverage
+ tools/expand
+ tools/flank
+ tools/genomecov
+ tools/getfasta
+ tools/groupby
+ tools/igv
+ tools/intersect
+ tools/jaccard
+ tools/links
+ tools/makewindows
+ tools/map
+ tools/maskfasta
+ tools/merge
+ tools/multicov
+ tools/multiinter
+ tools/nuc
+ tools/overlap
+ tools/pairtobed
+ tools/pairtopair
+ tools/random
+ tools/reldist
+ tools/shuffle
+ tools/slop
+ tools/sort
+ tools/subtract
+ tools/tag
+ tools/unionbedg
+ tools/window
\ No newline at end of file
diff --git a/docs/content/complementBed.rst b/docs/content/complementBed.rst
deleted file mode 100755
index 1951d0d..0000000
--- a/docs/content/complementBed.rst
+++ /dev/null
@@ -1,48 +0,0 @@
-###############
-5.17 complementBed
-###############
-**complementBed** returns the intervals in a genome that are not by the features in a feature file. An
-example usage of this tool would be to return the intervals of the genome that are not annotated as a
-repeat.
-
-
-==========================================================================
-5.17.1 Usage and option summary
-==========================================================================
-Usage:
-::
- complementBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
-
-**No additional options.**
-
-
-
-
-==========================================================================
-5.17.2 Default behavior
-==========================================================================
-Figure:
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BED FILE A ************* *************** ******************
-
- Result === === ===== =======
-
-
-For example:
-::
- cat A.bed
- chr1 100 200
- chr1 400 500
- chr1 500 800
-
- cat my.genome
- chr1 1000
-
- complementBed -i A.bed -g my.genome
- chr1 0 100
- chr1 200 400
- chr1 800 1000
-
-
diff --git a/docs/content/example-usage.rst b/docs/content/example-usage.rst
index 3fe5edf..43da749 100755
--- a/docs/content/example-usage.rst
+++ b/docs/content/example-usage.rst
@@ -1,331 +1,333 @@
###############
Example usage
###############
-Below are several examples of basic BEDTools usage. Example BED files are provided in the
-/data directory of the BEDTools distribution.
+
+Below are several examples of basic bedtools usage. Example BED files are
+provided in the /data directory of the bedtools distribution.
==========================================================================
-6.1 intersectBed
+bedtools intersect
==========================================================================
-6.1.1 Report the base-pair overlap between sequence alignments and genes.
-::
- intersectBed -a reads.bed -b genes.bed
-
-
+Report the base-pair overlap between sequence alignments and genes.
-6.1.2 Report whether each alignment overlaps one or more genes. If not, the alignment is not reported.
-::
- intersectBed -a reads.bed -b genes.bed -u
-
+.. code-block:: bash
+ bedtools intersect -a reads.bed -b genes.bed
-6.1.3 Report those alignments that overlap NO genes. Like "grep -v"
-::
- intersectBed -a reads.bed -b genes.bed -v
-6.1.4 Report the number of genes that each alignment overlaps.
-::
- intersectBed -a reads.bed -b genes.bed -c
+Report whether each alignment overlaps one or more genes. If not, the alignment is not reported.
+.. code-block:: bash
+
+ bedtools intersect -a reads.bed -b genes.bed -u
+
+
+Report those alignments that overlap NO genes. Like "grep -v"
-6.1.5 Report the entire, original alignment entry for each overlap with a gene.
-::
- intersectBed -a reads.bed -b genes.bed -wa
+.. code-block:: bash
+
+ bedtools intersect -a reads.bed -b genes.bed -v
+Report the number of genes that each alignment overlaps.
-6.1.6 Report the entire, original gene entry for each overlap with a gene.
-::
- intersectBed -a reads.bed -b genes.bed -wb
+.. code-block:: bash
+ bedtools intersect -a reads.bed -b genes.bed -c
-6.1.7 Report the entire, original alignment and gene entries for each overlap.
-::
- intersectBed -a reads.bed -b genes.bed -wa -wb
-
+Report the entire, original alignment entry for each overlap with a gene.
-
-6.1.8 Only report an overlap with a repeat if it spans at least 50% of the exon.
-::
- intersectBed -a exons.bed -b repeatMasker.bed -f 0.50
+.. code-block:: bash
+
+ bedtools intersect -a reads.bed -b genes.bed -wa
-6.1.9 Only report an overlap if comprises 50% of the structural variant and 50% of the segmental duplication. Thus, it is reciprocally at least a 50% overlap.
-::
- intersectBed -a SV.bed -b segmentalDups.bed -f 0.50 -r
+Report the entire, original gene entry for each overlap with a gene.
+.. code-block:: bash
+ bedtools intersect -a reads.bed -b genes.bed -wb
-6.1.10 Read BED A from stdin. For example, find genes that overlap LINEs but not SINEs.
-::
- intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v
-
-
+Report the entire, original alignment and gene entries for each overlap.
-6.1.11 Retain only single-end BAM alignments that overlap exons.
-::
- intersectBed -abam reads.bam -b exons.bed > reads.touchingExons.bam
-
-
-
+.. code-block:: bash
+ bedtools intersect -a reads.bed -b genes.bed -wa -wb
-6.1.12 Retain only single-end BAM alignments that do not overlap simple sequence
-repeats.
-::
- intersectBed -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam
+Only report an overlap with a repeat if it spans at least 50% of the exon.
-==========================================================================
-6.2 pairToBed
-==========================================================================
+.. code-block:: bash
+
+ bedtools intersect -a exons.bed -b repeatMasker.bed -f 0.50
-6.2.1 Return all structural variants (in BEDPE format) that overlap with genes on either
-end.
-::
- pairToBed -a sv.bedpe -b genes > sv.genes
+Only report an overlap if comprises 50% of the structural variant and 50% of the segmental duplication. Thus, it is reciprocally at least a 50% overlap.
+.. code-block:: bash
+
+ bedtools intersect -a SV.bed -b segmentalDups.bed -f 0.50 -r
-6.2.2 Return all structural variants (in BEDPE format) that overlap with genes on both
-end.
-::
- pairToBed -a sv.bedpe -b genes -type both > sv.genes
+Read BED A from stdin. For example, find genes that overlap LINEs but not SINEs.
+.. code-block:: bash
+ bedtools intersect -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed -v
-6.2.3 Retain only paired-end BAM alignments where neither end overlaps simple
-sequence repeats.
-::
- pairToBed -abam reads.bam -b SSRs.bed -type neither > reads.noSSRs.bam
-
-6.2.4 Retain only paired-end BAM alignments where both ends overlap segmental
-duplications.
-::
- pairToBed -abam reads.bam -b segdups.bed -type both > reads.SSRs.bam
+Retain only single-end BAM alignments that overlap exons.
+.. code-block:: bash
-
-
-6.2.5 Retain only paired-end BAM alignments where neither or one and only one end
-overlaps segmental duplications.
-::
- pairToBed -abam reads.bam -b segdups.bed -type notboth > reads.notbothSSRs.bam
+ bedtools intersect -abam reads.bam -b exons.bed > reads.touchingExons.bam
-
-
-
-
-==========================================================================
-6.3 pairToPair
-==========================================================================
+Retain only single-end BAM alignments that do not overlap simple sequence
+repeats.
-6.3.1 Find all SVs (in BEDPE format) in sample 1 that are also in sample 2.
-::
- pairToPair -a 1.sv.bedpe -b 2.sv.bedpe | cut -f 1-10 > 1.sv.in2.bedpe
+.. code-block:: bash
+
+ bedtools intersect -abam reads.bam -b SSRs.bed -v > reads.noSSRs.bam
-6.3.2 Find all SVs (in BEDPE format) in sample 1 that are not in sample 2.
-::
- pairToPair -a 1.sv.bedpe -b 2.sv.bedpe -type neither | cut -f 1-10 >
-1.sv.notin2.bedpe
+==========================================================================
+bedtools bamtobed
+==========================================================================
+Convert BAM alignments to BED format.
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam > reads.bed
-==========================================================================
-6.4 bamToBed
-==========================================================================
+Convert BAM alignments to BED format using the BAM edit distance (NM) as the
+BED "score".
-6.4.1 Convert BAM alignments to BED format.
-::
- bamToBed -i reads.bam > reads.bed
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam -ed > reads.bed
-6.4.2 Convert BAM alignments to BED format using the BAM edit distance (NM) as the
-BED "score".
-::
- bamToBed -i reads.bam -ed > reads.bed
+Convert BAM alignments to BEDPE format.
-6.4.3 Convert BAM alignments to BEDPE format.
-::
- bamToBed -i reads.bam -bedpe > reads.bedpe
+.. code-block:: bash
+
+ bedtools bamtobed -i reads.bam -bedpe > reads.bedpe
==========================================================================
-6.5 windowBed
+bedtools window
==========================================================================
-6.5.1 Report all genes that are within 10000 bp upstream or downstream of CNVs.
-::
- windowBed -a CNVs.bed -b genes.bed -w 10000
+Report all genes that are within 10000 bp upstream or downstream of CNVs.
+
+.. code-block:: bash
+
+ bedtools window -a CNVs.bed -b genes.bed -w 10000
-6.5.2 Report all genes that are within 10000 bp upstream or 5000 bp downstream of
+Report all genes that are within 10000 bp upstream or 5000 bp downstream of
CNVs.
-::
- windowBed -a CNVs.bed -b genes.bed -l 10000 -r 5000
+.. code-block:: bash
+
+ bedtools window -a CNVs.bed -b genes.bed -l 10000 -r 5000
-6.5.3 Report all SNPs that are within 5000 bp upstream or 1000 bp downstream of genes.
+
+Report all SNPs that are within 5000 bp upstream or 1000 bp downstream of genes.
Define upstream and downstream based on strand.
-::
- windowBed -a genes.bed -b snps.bed -l 5000 -r 1000 -sw
+
+.. code-block:: bash
+
+ bedtools window -a genes.bed -b snps.bed -l 5000 -r 1000 -sw
==========================================================================
-6.6 closestBed
+bedtools closest
==========================================================================
Note: By default, if there is a tie for closest, all ties will be reported. **closestBed** allows overlapping
features to be the closest.
-6.6.1 Find the closest ALU to each gene.
-::
- closestBed -a genes.bed -b ALUs.bed
+Find the closest ALU to each gene.
+
+.. code-block:: bash
+
+ bedtools closest -a genes.bed -b ALUs.bed
-6.6.2 Find the closest ALU to each gene, choosing the first ALU in the file if there is a
+
+Find the closest ALU to each gene, choosing the first ALU in the file if there is a
tie.
-::
- closestBed -a genes.bed -b ALUs.bed -t first
+
+.. code-block:: bash
+
+ bedtools closest -a genes.bed -b ALUs.bed -t first
-6.6.3 Find the closest ALU to each gene, choosing the last ALU in the file if there is a
+Find the closest ALU to each gene, choosing the last ALU in the file if there is a
tie.
-::
- closestBed -a genes.bed -b ALUs.bed -t last
+
+.. code-block:: bash
+
+ bedtools closest -a genes.bed -b ALUs.bed -t last
+
+
-
-
-
==========================================================================
-6.7 subtractBed
+bedtools subtract
==========================================================================
-Note: If a feature in A is entirely "spanned" by any feature in B, it will not be reported.
+.. note::
+
+ If a feature in A is entirely "spanned" by any feature in B, it will not be reported.
+
+Remove introns from gene features. Exons will (should) be reported.
+.. code-block:: bash
-6.7.1 Remove introns from gene features. Exons will (should) be reported.
-::
- subtractBed -a genes.bed -b introns.bed
+ bedtools subtract -a genes.bed -b introns.bed
==========================================================================
-6.8 mergeBed
+bedtools merge
==========================================================================
+.. note::
-6.8.1 Merge overlapping repetitive elements into a single entry.
-::
- mergeBed -i repeatMasker.bed
+ ``merge`` requires that the input is sorted by chromosome and then by start
+ coordinate. For example, for BED files, one would first sort the input
+ as follows: ``sort -k1,1 -k2,2n input.bed > input.sorted.bed``
+Merge overlapping repetitive elements into a single entry.
+.. code-block:: bash
-6.8.2 Merge overlapping repetitive elements into a single entry, returning the number of
+ bedtools merge -i repeatMasker.bed
+
+
+
+Merge overlapping repetitive elements into a single entry, returning the number of
entries merged.
-::
- mergeBed -i repeatMasker.bed -n
+
+.. code-block:: bash
+
+ bedtools merge -i repeatMasker.bed -n
-6.8.3 Merge nearby (within 1000 bp) repetitive elements into a single entry.
-::
- mergeBed -i repeatMasker.bed -d 1000
+Merge nearby (within 1000 bp) repetitive elements into a single entry.
+
+.. code-block:: bash
+
+ bedtools merge -i repeatMasker.bed -d 1000
==========================================================================
-6.9 coverageBed
+bedtools coverage
==========================================================================
-6.9.1 Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
+Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
genome.
-::
- coverageBed -a reads.bed -b windows10kb.bed | head
+
+.. code-block:: bash
+
+ bedtools coverage -a reads.bed -b windows10kb.bed | head
chr1 0 10000 0 10000 0.00
chr1 10001 20000 33 10000 0.21
chr1 20001 30000 42 10000 0.29
chr1 30001 40000 71 10000 0.36
-
-6.9.2 Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
+
+Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
genome and created a BEDGRAPH of the number of aligned reads in each window for
display on the UCSC browser.
-::
- coverageBed -a reads.bed -b windows10kb.bed | cut -f 1-4 > windows10kb.cov.bedg
+
+.. code-block:: bash
+
+ bedtools coverage -a reads.bed -b windows10kb.bed | cut -f 1-4 > windows10kb.cov.bedg
-6.9.3 Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
+Compute the coverage of aligned sequences on 10 kilobase "windows" spanning the
genome and created a BEDGRAPH of the fraction of each window covered by at least
one aligned read for display on the UCSC browser.
-::
- coverageBed -a reads.bed -b windows10kb.bed | awk ��{OFS="\t"; print $1,$2,$3,$6}��
- > windows10kb.pctcov.bedg
+
+.. code-block:: bash
+
+ bedtools coverage -a reads.bed -b windows10kb.bed | \
+ awk '{OFS="\t"; print $1,$2,$3,$6}' \
+ > windows10kb.pctcov.bedg
==========================================================================
-6.10 complementBed
+bedtools complement
==========================================================================
-6.10.1 Report all intervals in the human genome that are not covered by repetitive
+Report all intervals in the human genome that are not covered by repetitive
elements.
-::
- complementBed -i repeatMasker.bed -g hg18.genome
+
+.. code-block:: bash
+
+ bedtools complement -i repeatMasker.bed -g hg18.genome
==========================================================================
-6.11 shuffleBed
+bedtools shuffle
==========================================================================
-6.11.1 Randomly place all discovered variants in the genome. However, prevent them
+Randomly place all discovered variants in the genome. However, prevent them
from being placed in know genome gaps.
-::
- shuffleBed -i variants.bed -g hg18.genome -excl genome_gaps.bed
+
+.. code-block:: bash
+
+ bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed
-6.11.2 Randomly place all discovered variants in the genome. However, prevent them
+
+Randomly place all discovered variants in the genome. However, prevent them
from being placed in know genome gaps and require that the variants be randomly
placed on the same chromosome.
-::
- shuffleBed -i variants.bed -g hg18.genome -excl genome_gaps.bed -chrom
+
+.. code-block:: bash
+
+ bedtools shuffle -i variants.bed -g hg18.genome -excl genome_gaps.bed -chrom
diff --git a/docs/content/faq.rst b/docs/content/faq.rst
new file mode 100644
index 0000000..8999d81
--- /dev/null
+++ b/docs/content/faq.rst
@@ -0,0 +1,169 @@
+############
+FAQ
+############
+
+
+====================
+Installation issues
+====================
+
+--------------------------------------------------
+Why am I getting all of these zlib errors?
+--------------------------------------------------
+
+On certain operating systems (especially free Linux distributions) the complete
+zlib libraries are not installed. Bedtools depends upon zlib in order to
+decompress gzipped files.
+
+.. code-block:: bash
+
+ - Building main bedtools binary.
+ obj/gzstream.o: In function gzstreambuf::open(char const*, int):
+ gzstream.C:(.text+0x2a5): undefined reference to gzopen64'
+ collect2: ld returned 1 exit status
+ make: *** [all] Error 1
+
+If you see an error such as the above, it suggests you need to install the
+``zlib`` and ``zlib1g-dev`` libraries. This is typically straightforward using
+package managers. For example, on Debian/Ubuntu this would be:
+
+.. code-block:: bash
+
+ apt-get install zlib
+ apt-get install zlib1g-dev
+
+and on Fedora/Centos this would be:
+
+.. code-block:: bash
+
+ yum install zlib
+ yum install zlib1g-dev
+
+
+
+====================
+General questions
+====================
+
+
+--------------------------------------------------
+How do I know what version of bedtools I am using?
+--------------------------------------------------
+
+Use the --version option.
+
+.. code-block:: bash
+
+ $ bedtools --version
+ bedtools v2.17.0
+
+
+--------------------------------------------------
+How do I bring up the help/usage menu?
+--------------------------------------------------
+
+To receive a high level list of available tools in bedtools, use ```-h``:
+
+.. code-block:: bash
+
+ $ bedtools -h
+ bedtools: flexible tools for genome arithmetic and DNA sequence analysis.
+ usage: bedtools <subcommand> [options]
+
+ The bedtools sub-commands include:
+
+ [ Genome arithmetic ]
+ intersect Find overlapping intervals in various ways.
+ window Find overlapping intervals within a window around an interval.
+ closest Find the closest, potentially non-overlapping interval.
+ coverage Compute the coverage over defined intervals.
+ map Apply a function to a column for each overlapping interval.
+ genomecov Compute the coverage over an entire genome.
+ merge Combine overlapping/nearby intervals into a single interval.
+ cluster Cluster (but don't merge) overlapping/nearby intervals.
+ complement Extract intervals _not_ represented by an interval file.
+ ...
+
+To display the help for a specific tool (e.g., ``bedtools shuffle``), use:
+
+.. code-block:: bash
+
+ $ bedtools merge -h
+
+ Tool: bedtools merge (aka mergeBed)
+ Version: v2.17.0
+ Summary: Merges overlapping BED/GFF/VCF entries into a single interval.
+
+ Usage: bedtools merge [OPTIONS] -i <bed/gff/vcf>
+
+ Options:
+ -s Force strandedness. That is, only merge features
+ that are the same strand.
+ - By default, merging is done without respect to strand.
+
+ -n Report the number of BED entries that were merged.
+ - Note: "1" is reported if no merging occurred.
+
+
+
+
+
+====================
+Issues with output
+====================
+
+------------------------------------------------------------------------
+I *know* there are overlaps, but none are reported. What might be wrong?
+------------------------------------------------------------------------
+
+There are two common causes of this problem. The first cause is non-obvious
+differences in the way chromosomes are named in files being compared.
+For example, "1" is not the same as "chr1" just as " chr1" is not the same
+as "chr1". Secondly, users often copy files from a Windows machine to a UNIX
+machine. This causes issues because Windows uses two bytes to represent
+the end of a line (``\r\n``) whereas the UNIX convention uses a single byte
+(``\n``). If your files don't conform to the UNIX convention, you will have
+problems. One can convert files from Windows to UNIX with
+the following command:
+
+.. code-block:: bash
+
+ perl -i -p -e 's/\r\n/\n/g;' file.windows > file.unix
+
+
+
+====================
+Installation issues
+====================
+
+
+---------------------------------------------------------------------------
+Bedtools compilation fails with errors related to zlib. How do I fix this?
+---------------------------------------------------------------------------
+
+Some systems, especially Ubuntu, do not come pre-installed with up to date
+versions of the zlib compression utilities that tools such as `bedtools` and
+`samtools` depend upon. This can cause compilation errors when you try to
+compile `bedtools`. Errors include:
+
+.. code-block:: bash
+
+ ../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type
+
+
+or
+
+.. code-block:: bash
+
+ fatal error: zlib.h: No such file or directory
+
+This indicates that you need to install the zlib libraries on your system, which
+turns out to not be too difficult through the use of package installers. For
+example, on Ubuntu, you'd want to run:
+
+.. code-block:: bash
+
+ sudo apt-get install zlib1g-dev
+ sudo apt-get install zlib
+
+
diff --git a/docs/content/fastafromBed.rst b/docs/content/fastafromBed.rst
deleted file mode 100755
index 6e2b4ca..0000000
--- a/docs/content/fastafromBed.rst
+++ /dev/null
@@ -1,126 +0,0 @@
-###############
-5.11 fastaFromBed
-###############
-**fastaFromBed** extracts sequences from a FASTA file for each of the intervals defined in a BED file.
-The headers in the input FASTA file must exactly match the chromosome column in the BED file.
-
-==========================================================================
-5.11.1 Usage and option summary
-==========================================================================
-Usage:
-::
- fastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-name** Use the "name" column in the BED file for the FASTA headers in the output FASTA file.
-**-tab** Report extract sequences in a tab-delimited format instead of in FASTA format.
-**-s** Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. *Default: strand information is ignored*.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-
-
-==========================================================================
-5.11.2 Default behavior
-==========================================================================
-**fastaFromBed** will extract the sequence defined by the coordinates in a BED interval and create a
-new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each
-extracted sequence will be formatted as follows: "<chrom>:<start>-<end>".
-
-For example:
-::
- $ cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 5 10
-
- fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out
-
- cat test.fa.out
- >chr1:5-10
- AAACC
-
-
-
-
-==========================================================================
-5.11.3 Using the BED "name" column as a FASTA header.
-==========================================================================
-Using the **-name** option, one can set the FASTA header for each extracted sequence to be the "name"
-columns from the BED feature.
-
-For example:
-::
- cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 5 10 myseq
-
- fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out -name
-
- cat test.fa.out
- >myseq
- AAACC
-
-
-
-
-
-
-
-
-
-
-==========================================================================
-5.11.4 Creating a tab-delimited output file in lieu of FASTA output.
-==========================================================================
-Using the **-tab** option, the **-fo** output file will be tab-delimited instead of in FASTA format.
-
-For example:
-::
- cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 5 10 myseq
-
- fastaFromBed -fi test.fa -bed test.bed -fo test.fa.out.tab -name -tab
-
- cat test.fa.out
- myseq AAACC
-
-
-
-==========================================================================
-5.11.5 (-s)Forcing the extracted sequence to reflect the requested strand
-==========================================================================
-**fastaFromBed** will extract the sequence in the orientation defined in the strand column when the "-s"
-option is used.
-
-For example:
-::
- cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 20 25 forward 1 +
- chr1 20 25 reverse 1 -
-
- fastaFromBed -fi test.fa -bed test.bed -s -name -fo test.fa.out
-
- cat test.fa.out
- >forward
- CGCTA
- >reverse
- TAGCG
diff --git a/docs/content/general-usage.rst b/docs/content/general-usage.rst
index 7047cc5..910f3ea 100755
--- a/docs/content/general-usage.rst
+++ b/docs/content/general-usage.rst
@@ -3,73 +3,103 @@ General usage
###############
=======================
-4.1 Supported file formats
+Supported file formats
=======================
----------------------
-4.1.1 BED format
+BED format
----------------------
As described on the UCSC Genome Browser website (see link below), the BED format is a concise and
flexible way to represent genomic features and annotations. The BED format description supports up to
12 columns, but only the first 3 are required for the UCSC browser, the Galaxy browser and for
-BEDTools. BEDTools allows one to use the "BED12" format (that is, all 12 fields listed below).
+bedtools. bedtools allows one to use the "BED12" format (that is, all 12 fields listed below).
However, only intersectBed, coverageBed, genomeCoverageBed, and bamToBed will obey the BED12
"blocks" when computing overlaps, etc., via the **"-split"** option. For all other tools, the last six columns
-are not used for any comparisons by the BEDTools. Instead, they will use the entire span (start to end)
+are not used for any comparisons by the bedtools. Instead, they will use the entire span (start to end)
of the BED12 entry to perform any relevant feature comparisons. The last six columns will be reported
in the output of all comparisons.
The file description below is modified from: http://genome.ucsc.edu/FAQ/FAQformat#format1.
1. **chrom** - The name of the chromosome on which the genome feature exists.
- - *Any string can be used*. For example, "chr1", "III", "myChrom", "contig1112.23".
- - *This column is required*.
+
+ - *Any string can be used*. For example, "chr1", "III", "myChrom", "contig1112.23".
+ - *This column is required*.
+
2. **start** - The zero-based starting position of the feature in the chromosome.
+
- *The first base in a chromosome is numbered 0*.
- *The start position in each BED feature is therefore interpreted to be 1 greater than the start position listed in the feature. For example, start=9, end=20 is interpreted to span bases 10 through 20,inclusive*.
- *This column is required*.
+
3. **end** - The one-based ending position of the feature in the chromosome.
+
- *The end position in each BED feature is one-based. See example above*.
- *This column is required*.
+
4. **name** - Defines the name of the BED feature.
+
- *Any string can be used*. For example, "LINE", "Exon3", "HWIEAS_0001:3:1:0:266#0/1", or "my_Feature".
- *This column is optional*.
-5. **score** - The UCSC definition requires that a BED score range from 0 to 1000, inclusive. However, BEDTools allows any string to be stored in this field in order to allow greater flexibility in annotation features. For example, strings allow scientific notation for p-values, mean enrichment values, etc. It should be noted that this flexibility could prevent such annotations from being correctly displayed on the UCSC browser.
+
+5. **score** - The UCSC definition requires that a BED score range from 0 to 1000, inclusive. However, bedtools allows any string to be stored in this field in order to allow greater flexibility in annotation features. For example, strings allow scientific notation for p-values, mean enrichment values, etc. It should be noted that this flexibility could prevent such annotations from being correctly displayed on the UCSC browser.
+
- *Any string can be used*. For example, 7.31E-05 (p-value), 0.33456 (mean enrichment value), "up", "down", etc.
- *This column is optional*.
+
6. **strand** - Defines the strand - either '+' or '-'.
+
- *This column is optional*.
+
7. **thickStart** - The starting position at which the feature is drawn thickly.
- - *Allowed yet ignored by BEDTools*.
+
+ - *Allowed yet ignored by bedtools*.
+
8. **thickEnd** - The ending position at which the feature is drawn thickly.
- - *Allowed yet ignored by BEDTools*.
+
+ - *Allowed yet ignored by bedtools*.
+
9. **itemRgb** - An RGB value of the form R,G,B (e.g. 255,0,0).
- - *Allowed yet ignored by BEDTools*.
+
+ - *Allowed yet ignored by bedtools*.
+
10. **blockCount** - The number of blocks (exons) in the BED line.
- - *Allowed yet ignored by BEDTools*.
+
+ - *Allowed yet ignored by bedtools*.
+
11. **blockSizes** - A comma-separated list of the block sizes.
- - *Allowed yet ignored by BEDTools*.
+
+
12. **blockStarts** - A comma-separated list of block starts.
- - *Allowed yet ignored by BEDTools*.
+
+ - *Allowed yet ignored by bedtools*.
-BEDTools requires that all BED input files (and input received from stdin) are **tab-delimited**. The following types of BED files are supported by BEDTools:
+bedtools requires that all BED input files (and input received from stdin) are **tab-delimited**. The following types of BED files are supported by bedtools:
-1. | **BED3**: A BED file where each feature is described by **chrom**, **start**, and **end**.
- | For example: chr1 11873 14409
-2. | **BED4**: A BED file where each feature is described by **chrom**, **start**, **end**, and **name**.
- | For example: chr1 11873 14409 uc001aaa.3
-3. | **BED5**: A BED file where each feature is described by **chrom**, **start**, **end**, **name**, and **score**.
- | For example: chr1 11873 14409 uc001aaa.3 0
-4. | **BED6**: A BED file where each feature is described by **chrom**, **start**, **end**, **name**, **score**, and **strand**.
- | For example: chr1 11873 14409 uc001aaa.3 0 +
-5. | **BED12**: A BED file where each feature is described by all twelve columns listed above.
- | For example: chr1 11873 14409 uc001aaa.3 0 + 11873
- | 11873 0 3 354,109,1189, 0,739,1347,
+1. **BED3**: A BED file where each feature is described by **chrom**, **start**, and **end**.
+
+ For example: ``chr1 11873 14409``
+
+2. **BED4**: A BED file where each feature is described by **chrom**, **start**, **end**, and **name**.
+
+ For example: ``chr1 11873 14409 uc001aaa.3``
+
+3. **BED5**: A BED file where each feature is described by **chrom**, **start**, **end**, **name**, and **score**.
+
+ For example: ``chr1 11873 14409 uc001aaa.3 0``
+
+4. **BED6**: A BED file where each feature is described by **chrom**, **start**, **end**, **name**, **score**, and **strand**.
+
+ For example: ``chr1 11873 14409 uc001aaa.3 0 +``
+
+5. **BED12**: A BED file where each feature is described by all twelve columns listed above.
+
+ For example: ``chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347,``
----------------------
-4.1.2 BEDPE format
+BEDPE format
----------------------
We have defined a new file format (BEDPE) in order to concisely describe disjoint genome features,
such as structural variations or paired-end sequence alignments. We chose to define a new format
@@ -80,86 +110,127 @@ alignments, especially when studying structural variation.
The BEDPE format is described below. The description is modified from: http://genome.ucsc.edu/FAQ/FAQformat#format1.
1. **chrom1** - The name of the chromosome on which the **first** end of the feature exists.
+
- *Any string can be used*. For example, "chr1", "III", "myChrom", "contig1112.23".
- *This column is required*.
- *Use "." for unknown*.
+
2. **start1** - The zero-based starting position of the **first** end of the feature on **chrom1**.
+
- *The first base in a chromosome is numbered 0*.
- *As with BED format, the start position in each BEDPE feature is therefore interpreted to be 1 greater than the start position listed in the feature. This column is required*.
- *Use -1 for unknown*.
+
3. **end1** - The one-based ending position of the first end of the feature on **chrom1**.
+
- *The end position in each BEDPE feature is one-based*.
- *This column is required*.
- *Use -1 for unknown*.
+
4. **chrom2** - The name of the chromosome on which the **second** end of the feature exists.
+
- *Any string can be used*. For example, "chr1", "III", "myChrom", "contig1112.23".
- *This column is required*.
- *Use "." for unknown*.
+
5. **start2** - The zero-based starting position of the **second** end of the feature on **chrom2**.
+
- *The first base in a chromosome is numbered 0*.
- *As with BED format, the start position in each BEDPE feature is therefore interpreted to be 1 greater than the start position listed in the feature. This column is required*.
- *Use -1 for unknown*.
+
6. **end2** - The one-based ending position of the **second** end of the feature on **chrom2**.
+
- *The end position in each BEDPE feature is one-based*.
- *This column is required*.
- *Use -1 for unknown*.
+
7. **name** - Defines the name of the BEDPE feature.
+
- *Any string can be used*. For example, "LINE", "Exon3", "HWIEAS_0001:3:1:0:266#0/1", or "my_Feature".
- *This column is optional*.
-8. **score** - The UCSC definition requires that a BED score range from 0 to 1000, inclusive. *However, BEDTools allows any string to be stored in this field in order to allow greater flexibility in annotation features*. For example, strings allow scientific notation for p-values, mean enrichment values, etc. It should be noted that this flexibility could prevent such annotations from being correctly displayed on the UCSC browser.
+
+8. **score** - The UCSC definition requires that a BED score range from 0 to 1000, inclusive. *However, bedtools allows any string to be stored in this field in order to allow greater flexibility in annotation features*. For example, strings allow scientific notation for p-values, mean enrichment values, etc. It should be noted that this flexibility could prevent such annotations from being correctly displayed on the UCSC browser.
+
- *Any string can be used*. For example, 7.31E-05 (p-value), 0.33456 (mean enrichment value), "up", "down", etc.
- *This column is optional*.
+
9. **strand1** - Defines the strand for the first end of the feature. Either '+' or '-'.
+
- *This column is optional*.
- *Use "." for unknown*.
+
10. **strand2** - Defines the strand for the second end of the feature. Either '+' or '-'.
+
- *This column is optional*.
- *Use "." for unknown*.
-11. **Any number of additional, user-defined fields** - BEDTools allows one to add as many additional fields to the normal, 10-column BEDPE format as necessary. These columns are merely "passed through" **pairToBed** and **pairToPair** and are not part of any analysis. One would use these additional columns to add extra information (e.g., edit distance for each end of an alignment, or "deletion", "inversion", etc.) to each BEDPE feature.
+
+11. **Any number of additional, user-defined fields** - bedtools allows one to add as many additional fields to the normal, 10-column BEDPE format as necessary. These columns are merely "passed through" **pairToBed** and **pairToPair** and are not part of any analysis. One would use these additional columns to add extra information (e.g., edit distance for each end of an alignment, or "deletion", "inversion", etc.) to each BEDPE feature.
+
- *These additional columns are optional*.
Entries from an typical BEDPE file:
::
+
chr1 100 200 chr5 5000 5100 bedpe_example1 30 + -
chr9 1000 5000 chr9 3000 3800 bedpe_example2 100 + -
Entries from a BEDPE file with two custom fields added to each record:
::
+
chr1 10 20 chr5 50 60 a1 30 + - 0 1
chr9 30 40 chr9 80 90 a2 100 + - 2 1
----------------------
-4.1.3 GFF format
+GFF format
----------------------
-The GFF format is described on the Sanger Institute's website (http://www.sanger.ac.uk/resources/software/gff/spec.html). The GFF description below is modified from the definition at this URL. All nine columns in the GFF format description are required by BEDTools.
+The GFF format is described on the Sanger Institute's website (http://www.sanger.ac.uk/resources/software/gff/spec.html). The GFF description below is modified from the definition at this URL. All nine columns in the GFF format description are required by bedtools.
1. **seqname** - The name of the sequence (e.g. chromosome) on which the feature exists.
+
- *Any string can be used*. For example, "chr1", "III", "myChrom", "contig1112.23".
- *This column is required*.
+
2. **source** - The source of this feature. This field will normally be used to indicate the program making the prediction, or if it comes from public database annotation, or is experimentally verified, etc.
+
- *This column is required*.
+
3. **feature** - The feature type name. Equivalent to BED's **name** field.
+
- *Any string can be used*. For example, "exon", etc.
- *This column is required*.
+
4. **start** - The one-based starting position of feature on **seqname**.
+
- *This column is required*.
- - *BEDTools accounts for the fact the GFF uses a one-based position and BED uses a zero-based start position*.
+ - *bedtools accounts for the fact the GFF uses a one-based position and BED uses a zero-based start position*.
+
5. **end** - The one-based ending position of feature on **seqname**.
+
- *This column is required*.
-6. **score** - A score assigned to the GFF feature. Like BED format, BEDTools allows any string to be stored in this field in order to allow greater flexibility in annotation features. We note that this differs from the GFF definition in the interest of flexibility.
+
+6. **score** - A score assigned to the GFF feature. Like BED format, bedtools allows any string to be stored in this field in order to allow greater flexibility in annotation features. We note that this differs from the GFF definition in the interest of flexibility.
+
- *This column is required*.
+
7. **strand** - Defines the strand. Use '+', '-' or '.'
+
- *This column is required*.
+
8. **frame** - The frame of the coding sequence. Use '0', '1', '2', or '.'.
+
- *This column is required*.
-9. **attribute** - Taken from http://www.sanger.ac.uk/resources/software/gff/spec.html: From version 2 onwards, the attribute field must have an tag value structure following the syntax used within objects in a .ace file, flattened onto one line by semicolon separators. Tags must be standard identifiers ([A-Za-z][AZa-z0-9_]*). Free text values must be quoted with double quotes. *Note: all non-printing characters in such free text value strings (e.g. newlines, tabs, control characters, et [...]
+
+9. **attribute** - Taken from http://www.sanger.ac.uk/resources/software/gff/spec.html: From version 2 onwards, the attribute field must have an tag value structure following the syntax used within objects in a .ace file, flattened onto one line by semicolon separators. Free text values must be quoted with double quotes. *Note: all non-printing characters in such free text value strings (e.g. newlines, tabs, control characters, etc) must be explicitly represented by their C (UNIX) style [...]
+
- *This column is required*.
An entry from an example GFF file :
+
::
seq1 BLASTX similarity 101 235 87.1 + 0 Target "HBA_HUMAN" 11 55 ;
E_value 0.0003 dJ102G20 GD_mRNA coding_exon 7105 7201 . - 2 Sequence
@@ -167,17 +238,18 @@ An entry from an example GFF file :
-----------------------
-4.1.3 GFF format
-----------------------
-Some of the BEDTools (e.g., genomeCoverageBed, complementBed, slopBed) need to know the size of
+------------------------
+*Genome* file format
+------------------------
+Some of the bedtools (e.g., genomeCoverageBed, complementBed, slopBed) need to know the size of
the chromosomes for the organism for which your BED files are based. When using the UCSC Genome
Browser, Ensemble, or Galaxy, you typically indicate which which species/genome build you are
-working. The way you do this for BEDTools is to create a "genome" file, which simply lists the names of
+working. The way you do this for bedtools is to create a "genome" file, which simply lists the names of
the chromosomes (or scaffolds, etc.) and their size (in basepairs).
Genome files must be **tab-delimited** and are structured as follows (this is an example for *C. elegans*):
+
::
chrI 15072421
chrII 15279323
@@ -185,29 +257,28 @@ Genome files must be **tab-delimited** and are structured as follows (this is an
chrX 17718854
chrM 13794
-BEDTools includes pre-defined genome files for human and mouse in the **/genomes** directory included
-in the BEDTools distribution.
+bedtools includes pre-defined genome files for human and mouse in the **/genomes** directory included
+in the bedtools distribution.
----------------------
-4.1.5 SAM/BAM format
+SAM/BAM format
----------------------
The SAM / BAM format is a powerful and widely-used format for storing sequence alignment data (see
http://samtools.sourceforge.net/ for more details). It has quickly become the standard format to which
-most DNA sequence alignment programs write their output. Currently, the following BEDTools
-support inout in BAM format: *intersectBed, windowBed, coverageBed, genomeCoverageBed,
-pairToBed, bamToBed*. Support for the BAM format in BEDTools allows one to (to name a few):
+most DNA sequence alignment programs write their output. Currently, the following bedtools
+support input in BAM format: ``intersect``, ``window``, ``coverage``, ``genomecov``,
+``pairtobed``, ``bamtobed``. Support for the BAM format in bedtools allows one to (to name a few):
compare sequence alignments to annotations, refine alignment datasets, screen for potential mutations
and compute aligned sequence coverage.
-The details of how these tools work with BAM files are addressed in **Section 5** of this manual.
----------------------
-4.1.6 VCF format
+VCF format
----------------------
The Variant Call Format (VCF) was conceived as part of the 1000 Genomes Project as a standardized
means to report genetic variation calls from SNP, INDEL and structural variant detection programs
(see http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 for details).
-BEDTools now supports the latest version of this format (i.e, Version 4.0). As a result, BEDTools can
+bedtools now supports the latest version of this format (i.e, Version 4.0). As a result, bedtools can
be used to compare genetic variation calls with other genomic features.
diff --git a/docs/content/genomecoverageBed.rst b/docs/content/genomecoverageBed.rst
deleted file mode 100755
index 3c5d691..0000000
--- a/docs/content/genomecoverageBed.rst
+++ /dev/null
@@ -1,122 +0,0 @@
-###############
-5.10 genomeCoverageBed
-###############
-**genomeCoverageBed** computes a histogram of feature coverage (e.g., aligned sequences) for a given
-genome. Optionally, by using the **-d** option, it will report the depth of coverage at *each base* on each
-chromosome in the genome file (**-g**).
-
-==========================================================================
-5.10.1 Usage and option summary
-==========================================================================
-Usage:
-::
- genomeCoverageBed [OPTIONS] -i <BED> -g <GENOME>
-
-NOTE: genomeCoverageBed requires that the input BED file be sorted by
-chromosome. A simple sort -k1,1 will suffice.
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-ibam** BAM file as input for coverage. Each BAM alignment in A added to the total coverage for the genome. Use "stdin" if passing it with a UNIX pipe: For example:
- | samtools view -b <BAM> | genomeCoverageBed -ibam stdin -g hg18.genome
-**-d** Report the depth at each genome position. *Default behavior is to report a histogram*.
-**-max** Combine all positions with a depth >= max into a single bin in the histogram.
-**-bg** Report depth in BedGraph format. For details, see: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
-**-bga** Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: "grep -w 0$" to the output.
-**-split** Treat "split" BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).
-**-strand** Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6).
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-==========================================================================
-5.10.2 Default behavior
-==========================================================================
-By default, **genomeCoverageBed** will compute a histogram of coverage for the genome file provided.
-The default output format is as follows:
-1. chromosome (or entire genome)
-2. depth of coverage from features in input file
-3. number of bases on chromosome (or genome) with depth equal to column 2.
-4. size of chromosome (or entire genome) in base pairs
-5. fraction of bases on chromosome (or entire genome) with depth equal to column 2.
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 20 30
- chr2 0 500
-
- cat my.genome
- chr1 1000
- chr2 500
-
- genomeCoverageBed -i A.bed -g my.genome
- chr1 0 980 1000 0.98
- chr1 1 20 1000 0.02
- chr2 1 500 500 1
- genome 0 980 1500 0.653333
- genome 1 520 1500 0.346667
-
-
-
-
-==========================================================================
-5.10.3 (-max)Controlling the histogram's maximum depth
-==========================================================================
-Using the **-max** option, **genomeCoverageBed** will "lump" all positions in the genome having feature
-coverage greather than or equal to **max** into the **max** histogram bin. For example, if one sets **-max**
-equal to 50, the max depth reported in the output will be 50 and all positions with a depth >= 50 will
-be represented in bin 50.
-
-==========================================================================
-5.10.4 (-d)Reporting "per-base" genome coverage
-==========================================================================
-Using the **-d** option, **genomeCoverageBed** will compute the depth of feature coverage for each base
-on each chromosome in genome file provided.
-
-The "per-base" output format is as follows:
-1. chromosome
-2. chromosome position
-3. depth (number) of features overlapping this chromosome position.
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 20 30
- chr2 0 500
-
- cat my.genome
- chr1 1000
- chr2 500
-
- genomeCoverageBed -i A.bed -g my.genome -d | head -15 | tail -n 10
- chr1 6 0
- chr1 7 0
- chr1 8 0
- chr1 9 0
- chr1 10 0
- chr1 11 1
- chr1 12 1
- chr1 13 1
- chr1 14 1
- chr1 15 1
-
-
-
-==========================================================================
-5.1.13 (-split)Reporting coverage with spliced alignments or blocked BED features
-==========================================================================
-As described in section 1.3.19, genomeCoverageBed will, by default, screen for overlaps against the
-entire span of a spliced/split BAM alignment or blocked BED12 feature. When dealing with RNA-seq
-reads, for example, one typically wants to only screen for overlaps for the portions of the reads that
-come from exons (and ignore the interstitial intron sequence). The **-split** command allows for such
-overlaps to be performed.
-
-For additional details, please visit the Usage From The Wild site and have a look at example 5,
-contributed by Assaf Gordon.
-
-
diff --git a/docs/content/groupBy.rst b/docs/content/groupBy.rst
deleted file mode 100755
index 178f828..0000000
--- a/docs/content/groupBy.rst
+++ /dev/null
@@ -1,194 +0,0 @@
-###############
-5.22 groupBy
-###############
-**groupBy** is a useful tool that mimics the "groupBy" clause in database systems. Given a file or stream
-that is sorted by the appropriate "grouping columns", groupBy will compute summary statistics on
-another column in the file or stream. This will work with output from all BEDTools as well as any other
-tab-delimited file or stream.
-
-**NOTE: When using groupBy, the input data must be ordered by the same
-columns as specified with the -grp argument. For example, if -grp is 1,2,3, the the
-data should be pre-grouped accordingly. When groupBy detects changes in the
-group columns it then summarizes all lines with that group**.
-
-
-==========================================================================
-5.22.1 Usage and option summary
-==========================================================================
-Usage:
-::
- groupBy [OPTIONS] -i <input> -opCol <input column>
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-i** The input file that should be grouped and summarized. *Use "stdin" when using piped input*.
- **Note: if -i is omitted, input is assumed to come from standard input (stdin)**
-**-g OR -grp** Specifies which column(s) (1-based) should be used to group the input. The columns must be comma-separated and each column must be explicitly listed. No ranges (e.g. 1-4) yet allowed. *Default: 1,2,3*
-**-c OR -opCol** Specify the column (1-based) that should be summarized. *Required*.
-**-o OR -op** Specify the operation that should be applied to **opCol**.
-
- | Valid operations:
-
- | **sum** - *numeric only*
- | **count** - *numeric or text*
- | **min** - *numeric only*
- | **max** - *numeric only*
- | **mean** - *numeric only*
- | **stdev** - *numeric only*
- | **median** - *numeric only*
- | **mode** - *numeric or text*
- | **antimode** - *numeric or text*
- | **collapse** (i.e., print a comma separated list) - *numeric or text*
- | **freqasc** - *print a comma separated list of values observed and the number of times they were observed. Reported in ascending order of frequency*
- | **freqdesc** - *print a comma separated list of values observed and the number of times they were observed. Reported in descending order of frequency*
-
- | *Default: sum*
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-==========================================================================
-5.22.2 Default behavior.
-==========================================================================
-Let's imagine we have three incredibly interesting genetic variants that we are studying and we are
-interested in what annotated repeats these variants overlap.
-::
- cat variants.bed
- chr21 9719758 9729320 variant1
- chr21 9729310 9757478 variant2
- chr21 9795588 9796685 variant3
-
- intersectBed -a variants.bed -b repeats.bed -wa -wb > variantsToRepeats.bed
- cat variantsToRepeats.bed
- chr21 9719758 9729320 variant1 chr21 9719768 9721892 ALR/Alpha 1004 +
- chr21 9719758 9729320 variant1 chr21 9721905 9725582 ALR/Alpha 1010 +
- chr21 9719758 9729320 variant1 chr21 9725582 9725977 L1PA3 3288 +
- chr21 9719758 9729320 variant1 chr21 9726021 9729309 ALR/Alpha 1051 +
- chr21 9729310 9757478 variant2 chr21 9729320 9729809 L1PA3 3897 -
- chr21 9729310 9757478 variant2 chr21 9729809 9730866 L1P1 8367 +
- chr21 9729310 9757478 variant2 chr21 9730866 9734026 ALR/Alpha 1036 -
- chr21 9729310 9757478 variant2 chr21 9734037 9757471 ALR/Alpha 1182 -
- chr21 9795588 9796685 variant3 chr21 9795589 9795713 (GAATG)n 308 +
- chr21 9795588 9796685 variant3 chr21 9795736 9795894 (GAATG)n 683 +
- chr21 9795588 9796685 variant3 chr21 9795911 9796007 (GAATG)n 345 +
- chr21 9795588 9796685 variant3 chr21 9796028 9796187 (GAATG)n 756 +
- chr21 9795588 9796685 variant3 chr21 9796202 9796615 (GAATG)n 891 +
- chr21 9795588 9796685 variant3 chr21 9796637 9796824 (GAATG)n 621 +
-
-
-We can see that variant1 overlaps with 3 repeats, variant2 with 4 and variant3 with 6. We can use
-groupBy to summarize the hits for each variant in several useful ways. The default behavior is to
-compute the *sum* of the opCol.
-::
- groupBy -i variantsToRepeats.bed -grp 1,2,3 -opCol 9
- chr21 9719758 9729320 6353
- chr21 9729310 9757478 14482
- chr21 9795588 9796685 3604
-
-
-
-==========================================================================
-5.22.3 Computing the min and max.
-==========================================================================
-Now let's find the *min* and *max* repeat score for each variant. We do this by "grouping" on the variant
-coordinate columns (i.e. cols. 1,2 and 3) and ask for the min and max of the repeat score column (i.e.
-col. 9).
-::
- groupBy -i variantsToRepeats.bed -g 1,2,3 -c 9 -o min
- chr21 9719758 9729320 1004
- chr21 9729310 9757478 1036
- chr21 9795588 9796685 308
-
-We can also group on just the *name* column with similar effect.
-::
- groupBy -i variantsToRepeats.bed -grp 4 -opCol 9 -op min
- variant1 1004
- variant2 1036
- variant3 308
-
-What about the *max* score? Let's keep the coordinates and the name of the variants so that we
-stay in BED format.
-::
- groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op max
- chr21 9719758 9729320 variant1 3288
- chr21 9729310 9757478 variant2 8367
- chr21 9795588 9796685 variant3 891
-
-
-
-==========================================================================
-5.22.4 Computing the mean and median.
-==========================================================================
-Now let's find the *mean* and *median* repeat score for each variant.
-::
- cat variantsToRepeats.bed | groupBy -g 1,2,3,4 -c 9 -o mean
- chr21 9719758 9729320 variant1 1588.25
- chr21 9729310 9757478 variant2 3620.5
- chr21 9795588 9796685 variant3 600.6667
-
- groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op median
- chr21 9719758 9729320 variant1 1030.5
- chr21 9729310 9757478 variant2 2539.5
- chr21 9795588 9796685 variant3 652
-
-
-==========================================================================
-5.22.5 Computing the mode and "antimode".
-==========================================================================
-Now let's find the *mode* and *antimode* (i.e., the least frequent) repeat score for each variant (in this case
-they are identical).
-::
- groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op mode
- chr21 9719758 9729320 variant1 1004
- chr21 9729310 9757478 variant2 1036
- chr21 9795588 9796685 variant3 308
-
- groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op antimode
- chr21 9719758 9729320 variant1 1004
- chr21 9729310 9757478 variant2 1036
- chr21 9795588 9796685 variant3 308
-
-
-
-==========================================================================
-5.22.6 Computing the count of lines for a given group.
-==========================================================================
-Figure:
-::
- groupBy -i variantsToRepeats.bed -g 1,2,3,4 -c 9 -c count
- chr21 9719758 9729320 variant1 4
- chr21 9729310 9757478 variant2 4
- chr21 9795588 9796685 variant3 6
-
-
-
-
-==========================================================================
-5.22.7 Collapsing: listing all of the values in the opCol for a given group.
-==========================================================================
-Now for something different. What if we wanted all of the names of the repeats listed on the same line
-as the variants? Use the collapse option. This "denormalizes" things. Now you have a list of all the
-repeats on a single line.
-::
- groupBy -i variantsToRepeats.bed -grp 1,2,3,4 -opCol 9 -op collapse
- chr21 9719758 9729320 variant1 ALR/Alpha,ALR/Alpha,L1PA3,ALR/Alpha,
- chr21 9729310 9757478 variant2 L1PA3,L1P1,ALR/Alpha,ALR/Alpha,
- chr21 9795588 9796685 variant3 (GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,
-
-
-
-==========================================================================
-5.22.8 Computing frequencies: freqasc and freqdesc.
-==========================================================================
-Now for something different. What if we wanted all of the names of the repeats listed on the same line
-as the variants? Use the collapse option. This "denormalizes" things. Now you have a list of all the
-repeats on a single line.
-::
- cat variantsToRepeats.bed | groupBy -g 1 -c 8 -o freqdesc
- chr21 (GAATG)n:6,ALR/Alpha:5,L1PA3:2,L1P1:1,
-
- cat variantsToRepeats.bed | groupBy -g 1 -c 8 -o freqasc
- chr21 L1P1:1,L1PA3:2,ALR/Alpha:5,(GAATG)n:6,
\ No newline at end of file
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diff --git a/docs/content/installation.rst b/docs/content/installation.rst
index 675cb33..659c8db 100755
--- a/docs/content/installation.rst
+++ b/docs/content/installation.rst
@@ -2,24 +2,100 @@
Installation
############
-BEDTools is intended to run in a "command line" environment on UNIX, LINUX and Apple OS X
-operating systems. Installing BEDTools involves downloading the latest source code archive followed by
-compiling the source code into binaries on your local system. The following commands will install
-BEDTools in a local directory on a NIX or OS X machine. Note that the **"<version>"** refers to the
-latest posted version number on http://bedtools.googlecode.com/.
-
-Note: *The BEDTools "makefiles" use the GCC compiler. One should edit the Makefiles accordingly if
-one wants to use a different compiler.*::
-
- curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
- tar -zxvf BEDTools.tar.gz
- cd BEDTools-<version>
- make clean
- make all
- ls bin
+
+``bedtools`` is intended to run in a "command line" environment on UNIX, LINUX
+and Apple OS X operating systems. Installing ``bedtools`` involves either
+downloading the source code and compiling it manually, or installing stable
+release from package managers such as
+`homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_.
+
+
+
+
+--------------------------
+Installing stable releases
+--------------------------
+
+.....................................
+Compiling from source via Google Code
+.....................................
+
+Stable, versioned releases of bedtools are made available The following commands
+will install ``bedtools`` in a local directory on an UNIX or OS X machine.
+Note that the **"<version>"** refers to the latest posted version number
+on http://bedtools.googlecode.com/.
+
+.. note::
+
+ The bedtools Makefiles utilize the GCC compiler. One should edit the
+ Makefiles accordingly if one wants to use a different compiler.
+
+.. code-block:: bash
+
+ $ curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
+ $ tar -zxvf BEDTools.tar.gz
+ $ cd BEDTools-<version>
+ $ make
-At this point, one should copy the binaries in BEDTools/bin/ to either usr/local/bin/ or some
-other repository for commonly used UNIX tools in your environment. You will typically require
-administrator (e.g. "root" or "sudo") privileges to copy to usr/local/bin/. If in doubt, contact you
+At this point, one should copy the binaries in ./bin/ to either
+``usr/local/bin/`` or some other repository for commonly used UNIX tools in
+your environment. You will typically require administrator (e.g. "root" or
+"sudo") privileges to copy to ``usr/local/bin/``. If in doubt, contact you
system administrator for help.
+.....................................
+Installing with package managers
+.....................................
+
+In addition, stable releases of ``bedtools`` are also available through package
+managers such as `homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_,
+``apt-get`` and ``yum``.
+
+**Fedora/Centos**. Adam Huffman has created a Red Hat package for bedtools so
+that one can easily install the latest release using "yum", the Fedora
+package manager. It should work with Fedora 13, 14 and EPEL5/6 (
+for Centos, Scientific Linux, etc.).
+
+.. code-block:: bash
+
+ yum install BEDTools
+
+**Debian/Ubuntu.** Charles Plessy also maintains a Debian package for bedtools
+that is likely to be found in its derivatives like Ubuntu. Many thanks to
+Charles for doing this.
+
+.. code-block:: bash
+
+ apt-get install bedtools
+
+
+**Homebrew**. Carlos Borroto has made BEDTools available on the bedtools
+package manager for OSX.
+
+.. code-block:: bash
+
+ brew install bedtools
+
+
+
+-----------------------------
+Development versions
+-----------------------------
+
+The development version of bedtools is maintained in a Github
+`repository <https://www.github.com/arq5x/bedtools>`_. Bug fixes are addressed
+in this repository prior to release, so there may be situations where you will
+want to use a development version of bedtools prior to its being promoted to
+a stable release. One would either clone the repository with ``git``, as
+follows and then compile the source code as describe above:
+
+.. code-block:: bash
+
+ git clone https://github.com/arq5x/bedtools.git
+
+
+or, one can download the source code as a ``.zip`` file using the Github
+website. Once the zip file is downloaded and uncompressed with the ``unzip``
+command, one can compile and install using the instructions above.
+
+ .. image:: images/github-zip-button.png
diff --git a/docs/content/intersectBed.rst b/docs/content/intersectBed.rst
deleted file mode 100755
index db4632f..0000000
--- a/docs/content/intersectBed.rst
+++ /dev/null
@@ -1,385 +0,0 @@
-#########################################
-5.1 intersect
-#########################################
-
-By far, the most common question asked of two sets of genomic features is whether or not any of the
-features in the two sets "overlap" with one another. This is known as feature intersection. **bedtools intersect**
-allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have
-fine control as to how the intersections are reported. **bedtools intersect** works with both BED/GFF/VCF
-and BAM files as input.
-
-===============================
-5.1.1 Usage and option summary
-===============================
-**Usage**:
-::
-
- bedtools intersect [OPTIONS] [-a <BED/GFF/VCF> || -abam <BAM>] -b <BED/GFF/VCF>
-
- intersectBed [OPTIONS] [-a <BED/GFF/VCF> || -abam <BAM>] -b <BED/GFF/VCF>
-
-
-
-=========================== =========================================================================================================================================================
-Option Description
-=========================== =========================================================================================================================================================
-**-a** BED/GFF/VCF file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
-**-b** BED/GFF/VCF file B. Use "stdin" if passing B with a UNIX pipe.
-**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools intersect -abam stdin -b genes.bed
-**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
-**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: bedtools intersect -abam reads.bam -b genes.bed -bed
-**-wa** Write the original entry in A for each overlap.
-**-wb** Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.
-**-wo** Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by -f and -r.
-**-wao** Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by -f and -r.
-**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. Restricted by -f and -r.
-**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B. Restricted by -f and -r.
-**-v** Only report those entries in A that have no overlap in B. Restricted by -f and -r.
-**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
-**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
-**-split** Treat "split" BAM (i.e., having an "N" CIGAR operation) or BED12 entries as distinct BED intervals.
-=========================== =========================================================================================================================================================
-
-
-===============================
-5.1.2 Default behavior
-===============================
-By default, if an overlap is found, **bedtools intersect** reports the shared interval between the two
-overlapping features.
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
-
- bedtools intersect -a A.bed -b B.bed
- chr1 15 20
-
-.. plot::
-
- a = """chr1 10 20\nchr1 30 40"""
- b = """chr1 15 20"""
-
- title = "bedtools intersect -a A.bed -b B.bed"
- from matplotlib.pyplot import show
- from pyplots.plotter import plot_a_b_tool
- plot_a_b_tool(a, b, 'intersect', title, 'A.bed', 'B.bed')
- show()
-
-=============================================
-5.1.3 (-wa) Reporting the original A feature
-=============================================
-Instead, one can force **bedtools intersect** to report the *original* **"A"** feature when an overlap is found. As
-shown below, the entire "A" feature is reported, not just the portion that overlaps with the "B" feature.
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
-
- bedtools intersect -a A.bed -b B.bed -wa
- chr1 10 20
-
-.. plot::
-
- a = """chr1 10 20\nchr1 30 40"""
- b = """chr1 15 20"""
-
- title = "bedtools intersect -a A.bed -b B.bed -wa"
- from matplotlib.pyplot import show
- from pyplots.plotter import plot_a_b_tool
- plot_a_b_tool(a, b, 'intersect', title, 'A.bed', 'B.bed', wa=True)
- show()
-
-
-=============================================
-5.1.4 (-wb) Reporting the original B feature
-=============================================
-Similarly, one can force **bedtools intersect** to report the *original* **"B"** feature when an overlap is found. If
-just -wb is used, the overlapping portion of A will be reported followed by the *original* **"B"**. If both -wa
-and -wb are used, the *originals* of both **"A"** and **"B"** will be reported.
-
-For example (-wb alone):
-::
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
-
- bedtools intersect -a A.bed -b B.bed -wb
- chr1 15 20 chr 15 20
-
-
-Now -wa and -wb:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
-
- bedtools intersect -a A.bed -b B.bed -wa -wb
- chr1 10 20 chr 15 20
-
-=======================================================================
-5.1.5 (-u) Reporting the presence of *at least one* overlapping feature
-=======================================================================
-Frequently a feature in "A" will overlap with multiple features in "B". By default, **bedtools intersect** will
-report each overlap as a separate output line. However, one may want to simply know that there is at
-least one overlap (or none). When one uses the -u option, "A" features that overlap with one or more
-"B" features are reported once. Those that overlap with no "B" features are not reported at all.
-
-
-For example (*without* -u):
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
- chr1 18 25
-
- bedtools intersect -a A.bed -b B.bed -wb
- chr1 10 20 chr 15 20
- chr1 10 20 chr 18 25
-
-For example (*with* -u):
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
- chr1 18 25
-
- bedtools intersect -a A.bed -b B.bed -u
- chr1 10 20
-
-=======================================================================
-5.1.6 (-c) Reporting the number of overlapping features
-=======================================================================
-The -c option reports a column after each "A" feature indicating the *number* (0 or more) of overlapping
-features found in "B". Therefore, *each feature in A is reported once*.
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
- chr1 18 25
-
- bedtools intersect -a A.bed -b B.bed -u
- chr1 10 20 2
- chr1 30 40 0
-
-
-=======================================================================
-5.1.7 (-v) Reporting the absence of any overlapping features
-=======================================================================
-There will likely be cases where you'd like to know which "A" features do not overlap with any of the
-"B" features. Perhaps you'd like to know which SNPs don't overlap with any gene annotations. The -v
-(an homage to "grep -v") option will only report those "A" features that have no overlaps in "B".
-
-For example:
-::
- cat A.bed
- chr1 10 20
- chr1 30 40
-
- cat B.bed
- chr1 15 20
-
- bedtools intersect -a A.bed -b B.bed -v
- chr1 30 40
-
-.. plot::
-
- a = """chr1 10 20\nchr1 30 40"""
- b = """chr1 15 20"""
-
- title = "bedtools intersect -a A -b B -v"
- from matplotlib.pyplot import show
- from pyplots.plotter import plot_a_b_tool
- plot_a_b_tool(a, b, 'intersect', title, 'A.bed', 'B.bed', v=True)
- show()
-
-
-=======================================================================
-5.1.8 (-f) Requiring a minimal overlap fraction
-=======================================================================
-By default, **bedtools intersect** will report an overlap between A and B so long as there is at least one base
-pair is overlapping. Yet sometimes you may want to restrict reported overlaps between A and B to cases
-where the feature in B overlaps at least X% (e.g. 50%) of the A feature. The -f option does exactly
-this.
-
-For example (note that the second B entry is not reported):
-::
- cat A.bed
- chr1 100 200
-
- cat B.bed
- chr1 130 201
- chr1 180 220
-
- bedtools intersect -a A.bed -b B.bed -f 0.50 -wa -wb
- chr1 100 200 chr1 130 201
-
-==========================================================================
-5.1.9 (-r, combined with -f)Requiring reciprocal minimal overlap fraction
-==========================================================================
-Similarly, you may want to require that a minimal fraction of both the A and the B features is
-overlapped. For example, if feature A is 1kb and feature B is 1Mb, you might not want to report the
-overlap as feature A can overlap at most 1% of feature B. If one set -f to say, 0.02, and one also
-enable the -r (reciprocal overlap fraction required), this overlap would not be reported.
-
-For example (note that the second B entry is not reported):
-::
- cat A.bed
- chr1 100 200
-
- cat B.bed
- chr1 130 201
- chr1 130 200000
-
- bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
- chr1 100 200 chr1 130 201
-
-==========================================================================
-5.1.10 (-s)Enforcing "strandedness"
-==========================================================================
-By default, **bedtools intersect** will report overlaps between features even if the features are on opposite
-strands. However, if strand information is present in both BED files and the "-s" option is used, overlaps
-will only be reported when features are on the same strand.
-
-For example (note that the second B entry is not reported):
-::
- cat A.bed
- chr1 100 200 a1 100 +
-
- cat B.bed
- chr1 130 201 b1 100 -
- chr1 130 201 b2 100 +
-
- bedtools intersect -a A.bed -b B.bed -wa -wb -s
- chr1 100 200 a1 100 + chr1 130 201 b2 100 +
-
-
-==========================================================================
-5.1.11 (-abam)Default behavior when using BAM input
-==========================================================================
-When comparing alignments in BAM format (**-abam**) to features in BED format (**-b**), **bedtools intersect**
-will, **by default**, write the output in BAM format. That is, each alignment in the BAM file that meets
-the user's criteria will be written (to standard output) in BAM format. This serves as a mechanism to
-create subsets of BAM alignments are of biological interest, etc. Note that only the mate in the BAM
-alignment is compared to the BED file. Thus, if only one end of a paired-end sequence overlaps with a
-feature in B, then that end will be written to the BAM output. By contrast, the other mate for the
-pair will not be written. One should use **pairToBed(Section 5.2)** if one wants each BAM alignment
-for a pair to be written to BAM output.
-
-For example:
-::
- bedtools intersect -abam reads.unsorted.bam -b simreps.bed | samtools view - | head -3
-
- BERTHA_0001:3:1:15:1362#0 99 chr4 9236904 0 50M = 9242033 5 1 7 9
- AGACGTTAACTTTACACACCTCTGCCAAGGTCCTCATCCTTGTATTGAAG W c T U ] b \ g c e g X g f c b f c c b d d g g V Y P W W _
- \c`dcdabdfW^a^gggfgd XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:19 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:50
- BERTHA _0001:3:1:16:994#0 83 chr6 114221672 37 25S6M1I11M7S =
- 114216196 -5493 G A A A G G C C A G A G T A T A G A A T A A A C A C A A C A A T G T C C A A G G T A C A C T G T T A
- gffeaaddddggggggedgcgeggdegggggffcgggggggegdfggfgf XT:A:M NM:i:3 SM:i:37 AM:i:37 XM:i:2 X O : i :
- 1 XG:i:1 MD:Z:6A6T3
- BERTHA _0001:3:1:16:594#0 147 chr8 43835330 0 50M =
- 43830893 -4487 CTTTGGGAGGGCTTTGTAGCCTATCTGGAAAAAGGAAATATCTTCCCATG U
- \e^bgeTdg_Kgcg`ggeggg_gggggggggddgdggVg\gWdfgfgff XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:10 X1:i:7 X M : i :
- 2 XO:i:0 XG:i:0 MD:Z:1A2T45
-
-
-==========================================================================
-5.1.12 (-bed)Output BED format when using BAM input
-==========================================================================
-When comparing alignments in BAM format (**-abam**) to features in BED format (**-b**), **bedtools intersect**
-will **optionally** write the output in BED format. That is, each alignment in the BAM file is converted
-to a 6 column BED feature and if overlaps are found (or not) based on the user's criteria, the BAM
-alignment will be reported in BED format. The BED "name" field is comprised of the RNAME field in
-the BAM alignment. If mate information is available, the mate (e.g., "/1" or "/2") field will be
-appended to the name. The "score" field is the mapping quality score from the BAM alignment.
-
-For example:
-::
- bedtools intersect -abam reads.unsorted.bam -b simreps.bed -bed | head -20
-
- chr4 9236903 9236953 BERTHA_0001:3:1:15:1362#0/1 0 +
- chr6 114221671 114221721 BERTHA_0001:3:1:16:994#0/1 37 -
- chr8 43835329 43835379 BERTHA_0001:3:1:16:594#0/2 0 -
- chr4 49110668 49110718 BERTHA_0001:3:1:31:487#0/1 23 +
- chr19 27732052 27732102 BERTHA_0001:3:1:32:890#0/2 46 +
- chr19 27732012 27732062 BERTHA_0001:3:1:45:1135#0/1 37 +
- chr10 117494252 117494302 BERTHA_0001:3:1:68:627#0/1 37 -
- chr19 27731966 27732016 BERTHA_0001:3:1:83:931#0/2 9 +
- chr8 48660075 48660125 BERTHA_0001:3:1:86:608#0/2 37 -
- chr9 34986400 34986450 BERTHA_0001:3:1:113:183#0/2 37 -
- chr10 42372771 42372821 BERTHA_0001:3:1:128:1932#0/1 3 -
- chr19 27731954 27732004 BERTHA_0001:3:1:130:1402#0/2 0 +
- chr10 42357337 42357387 BERTHA_0001:3:1:137:868#0/2 9 +
- chr1 159720631 159720681 BERTHA_0001:3:1:147:380#0/2 37 -
- chrX 58230155 58230205 BERTHA_0001:3:1:151:656#0/2 37 -
- chr5 142612746 142612796 BERTHA_0001:3:1:152:1893#0/1 37 -
- chr9 71795659 71795709 BERTHA_0001:3:1:177:387#0/1 37 +
- chr1 106240854 106240904 BERTHA_0001:3:1:194:928#0/1 37 -
- chr4 74128456 74128506 BERTHA_0001:3:1:221:724#0/1 37 -
- chr8 42606164 42606214 BERTHA_0001:3:1:244:962#0/1 37 +
-
-==================================================================================
-5.1.13 (-split)Reporting overlaps with spliced alignments or blocked BED features
-==================================================================================
-As described in section 1.3.19, bedtools intersect will, by default, screen for overlaps against the entire span
-of a spliced/split BAM alignment or blocked BED12 feature. When dealing with RNA-seq reads, for
-example, one typically wants to only screen for overlaps for the portions of the reads that come from
-exons (and ignore the interstitial intron sequence). The **-split** command allows for such overlaps to be
-performed.
-
-For example, the diagram below illustrates the *default* behavior. The blue dots represent the "split/
-spliced" portion of the alignment (i.e., CIGAR "N" operation). In this case, the two exon annotations
-are reported as overlapping with the "split" BAM alignment, but in addition, a third feature that
-overlaps the "split" portion of the alignment is also reported.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Exons --------------- ----------
-
- BED/BAM A ************.......................................****
-
- BED File B ^^^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^
-
- Result =============== ======== ==========
-
-
-In contrast, when using the **-split** option, only the exon overlaps are reported.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Exons --------------- ----------
-
- BED/BAM A ************.......................................****
-
- BED File B ^^^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^
-
- Result =============== ==========
\ No newline at end of file
diff --git a/docs/content/maskfastafromBed.rst b/docs/content/maskfastafromBed.rst
deleted file mode 100755
index 1a8530e..0000000
--- a/docs/content/maskfastafromBed.rst
+++ /dev/null
@@ -1,70 +0,0 @@
-###############
-5.12 maskFastaFromBed
-###############
-**maskFastaFromBed** masks sequences in a FASTA file based on intervals defined in a feature file. The
-headers in the input FASTA file must exactly match the chromosome column in the feature file. This
-may be useful fro creating your own masked genome file based on custom annotations or for masking all
-but your target regions when aligning sequence data from a targeted capture experiment.
-
-
-==========================================================================
-5.12.1 Usage and option summary
-==========================================================================
-Usage:
-::
- maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
-
-NOTE: The input and output FASTA files must be different.
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-soft** Soft-mask (that is, convert to lower-case bases) the FASTA sequence. *By default, hard-masking (that is, conversion to Ns) is performed*.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-
-==========================================================================
-5.12.2 Default behavior
-==========================================================================
-**maskFastaFromBed** will mask a FASTA file based on the intervals in a BED file. The newly masked
-FASTA file is written to the output FASTA file.
-
-For example:
-::
- cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 5 10
-
- maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out
-
- cat test.fa.out
- >chr1
- AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
-
-==========================================================================
-5.12.3 Soft-masking the FASTA file.
-==========================================================================
-Using the **-soft** option, one can optionally "soft-mask" the FASTA file.
-
-For example:
-::
- cat test.fa
- >chr1
- AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
-
- cat test.bed
- chr1 5 10
-
- maskFastaFromBed -fi test.fa -bed test.bed -fo test.fa.out -soft
-
- cat test.fa.out
- >chr1
- AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
diff --git a/docs/content/mergeBed.rst b/docs/content/mergeBed.rst
deleted file mode 100755
index 16f73cc..0000000
--- a/docs/content/mergeBed.rst
+++ /dev/null
@@ -1,120 +0,0 @@
-###############
-5.8 mergeBed
-###############
-**mergeBed** combines overlapping or "book-ended" (that is, one base pair away) features in a feature file
-into a single feature which spans all of the combined features.
-
-==========================================================================
-5.8.1 Usage and option summary
-==========================================================================
-Usage:
-::
- mergeBed [OPTIONS] -i <BED/GFF/VCF>
-
-=========================== ===============================================================================================================================================================================================================
-Option Description
-=========================== ===============================================================================================================================================================================================================
-**-s** Force strandedness. That is, only merge features that are the same strand. *By default, this is disabled*.
-**-n** Report the number of BED entries that were merged. *1 is reported if no merging occurred*.
-**-d** Maximum distance between features allowed for features to be merged. *Default is 0. That is, overlapping and/or book-ended features are merged*.
-**-nms** Report the names of the merged features separated by semicolons.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-
-==========================================================================
-5.8.2 Default behavior
-==========================================================================
-Figure:
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BED FILE ************* *************** **********************
- ********
-
- Result =============================== ======================
-
-
-
-For example:
-::
- cat A.bed
- chr1 100 200
- chr1 180 250
- chr1 250 500
- chr1 501 1000
-
- mergeBed -i A.bed
- chr1 100 500
- chr1 501 1000
-
-
-
-
-
-
-==========================================================================
-5.8.3 (-s)Enforcing "strandedness"
-==========================================================================
-This option behaves the same as the -s option for intersectBed while scanning for features that should
-be merged. Only features on the same strand will be merged. See the discussion in the intersectBed
-section for details.
-
-==========================================================================
-5.8.4 (-n)Reporting the number of features that were merged
-==========================================================================
-The -n option will report the number of features that were combined from the original file in order to
-make the newly merged feature. If a feature in the original file was not merged with any other features,
-a "1" is reported.
-
-For example:
-::
- cat A.bed
- chr1 100 200
- chr1 180 250
- chr1 250 500
- chr1 501 1000
-
- mergeBed -i A.bed -n
- chr1 100 500 3
- chr1 501 1000 1
-
-
-==========================================================================
-5.8.5 (-d)Controlling how close two features must be in order to merge
-==========================================================================
-By default, only overlapping or book-ended features are combined into a new feature. However, one can
-force mergeBed to combine more distant features with the -d option. For example, were one to set -d to
-1000, any features that overlap or are within 1000 base pairs of one another will be combined.
-
-For example:
-::
- cat A.bed
- chr1 100 200
- chr1 501 1000
-
- mergeBed -i A.bed
- chr1 100 200
- chr1 501 1000
-
- mergeBed -i A.bed -d 1000
- chr1 100 200 1000
-
-==========================================================================
-5.8.6 (-nms)Reporting the names of the features that were merged
-==========================================================================
-Occasionally, one might like to know that names of the features that were merged into a new feature.
-The -nms option will add an extra column to the mergeBed output which lists (separated by
-semicolons) the names of the merged features.
-
-For example:
-::
- cat A.bed
- chr1 100 200 A1
- chr1 150 300 A2
- chr1 250 500 A3
-
- mergeBed -i A.bed -nms
- chr1 100 500 A1;A2;A3
diff --git a/docs/content/overview.rst b/docs/content/overview.rst
index a836365..3275cb2 100755
--- a/docs/content/overview.rst
+++ b/docs/content/overview.rst
@@ -1,73 +1,81 @@
-.. role:: red
-
############
Overview
############
==========
-1.1 Background
+Background
==========
-The development of BEDTools was motivated by a need for fast, flexible tools with which to compare large sets of genomic
+The development of bedtools was motivated by a need for fast, flexible tools with which to compare large sets of genomic
features. Answering fundamental research questions with existing tools was either too slow or required modifications to the
way they reported or computed their results. We were aware of the utilities on the UCSC Genome Browser and Galaxy websites, as
well as the elegant tools available as part of Jim Kent’s monolithic suite of tools (“Kent source”). However, we found that
the web-based tools were too cumbersome when working with large datasets generated by current sequencing technologies.
Similarly, we found that the Kent source command line tools often required a local installation of the UCSC Genome Browser.
These limitations, combined with the fact that we often wanted an extra option here or there that wasn’t available with
-existing tools, led us to develop our own from scratch. The initial version of BEDTools was publicly released in the spring of
+existing tools, led us to develop our own from scratch. The initial version of bedtools was publicly released in the spring of
2009. The current version has evolved from our research experiences and those of the scientists using the suite over the last
-year. The BEDTools suite enables one to answer common questions of genomic data in a fast and reliable manner. The fact that
+year. The bedtools suite enables one to answer common questions of genomic data in a fast and reliable manner. The fact that
almost all the utilities accept input from “stdin” allows one to “stream / pipe” several commands together to facilitate more
-complicated analyses. Also, the tools allow fine control over how output is reported. The initial version of BEDTools
+complicated analyses. Also, the tools allow fine control over how output is reported. The initial version of bedtools
supported solely 6-column `BED <http://genome.ucsc.edu/FAQ/FAQformat#format1>`_ files. *However, we have subsequently added support for sequence alignments in* `BAM <http://samtools.sourceforge.net/>`_
*format, as well as for features in* `GFF <http://genome.ucsc.edu/FAQ/FAQformat#format3>`_ , *“blocked” BED format, and*
`VCF <http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41>`_ *format*.
The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets. This manual seeks to describe the behavior and
-available functionality for each BEDTool. Usage examples are scattered throughout the text, and formal examples are
+available functionality for each bedtool. Usage examples are scattered throughout the text, and formal examples are
provided in the last two sections, we hope that this document will give you a sense of the flexibility of
-the toolkit and the types of analyses that are possible with BEDTools. If you have further questions, please join the BEDTools
+the toolkit and the types of analyses that are possible with bedtools. If you have further questions, please join the bedtools
discussion group, visit the Usage Examples on the Google Code site (usage, advanced usage), or take a look at the nascent
“Usage From the Wild” page.
===========================
-1.2 Summary of available tools.
+Summary of available tools.
===========================
-BEDTools support a wide range of operations for interrogating and manipulating genomic features. The table below summarizes
+bedtools support a wide range of operations for interrogating and manipulating genomic features. The table below summarizes
the tools available in the suite.
=========================== =========================================================================================================================================================
Utility Description
=========================== =========================================================================================================================================================
-**intersectBed** Returns overlaps between two BED/GFF/VCF files.
-**pairToBed** Returns overlaps between a paired-end BED file and a regular BED/VCF/GFF file.
-**bamToBed** Converts BAM alignments to BED6, BED12, or BEDPE format.
-**bedToBam** Converts BED/GFF/VCF features to BAM format.
-**bed12ToBed6** Converts "blocked" BED12 features to discrete BED6 features.
-**bedToIgv** Creates IGV batch scripts for taking multiple snapshots from BED/GFF/VCF features.
-**coverageBed** Summarizes the depth and breadth of coverage of features in one BED versus features (e.g, windows, exons, etc.) defined in another BED/GFF/VCF file.
-**multiBamCov** Counts sequence coverage for multiple position-sorted bams at specific loci defined in a BED/GFF/VCF file
-**tagBam** Annotates a BAM file with custom tag fields based on overlaps with BED/GFF/VCF files
-**nuclBed** Profiles the nucleotide content of intervals in a fasta file
-**genomeCoverageBed** Creates either a histogram, BEDGRAPH, or a "per base" report of genome coverage.
-**unionBedGraphs** Combines multiple BedGraph? files into a single file, allowing coverage/other comparisons between them.
-**annotateBed** Annotates one BED/VCF/GFF file with overlaps from many others.
-**groupBy** Deprecated. Now in the filo package.
-**overlap** Returns the number of bases pairs of overlap b/w two features on the same line.
-**pairToPair** Returns overlaps between two paired-end BED files.
-**closestBed** Returns the closest feature to each entry in a BED/GFF/VCF file.
-**subtractBed** Removes the portion of an interval that is overlapped by another feature.
-**windowBed** Returns overlaps between two BED/VCF/GFF files based on a user-defined window.
-**mergeBed** Merges overlapping features into a single feature.
-**complementBed** Returns all intervals not spanned by the features in a BED/GFF/VCF file.
-**fastaFromBed** Creates FASTA sequences based on intervals in a BED/GFF/VCF file.
-**maskFastaFromBed** Masks a FASTA file based on BED coordinates.
-**shuffleBed** Randomly permutes the locations of a BED file among a genome.
-**slopBed** Adjusts each BED entry by a requested number of base pairs.
-**flankBed** Creates flanking intervals for each feature in a BED/GFF/VCF file.
-**sortBed** Sorts a BED file by chrom, then start position. Other ways as well.
-**linksBed** Creates an HTML file of links to the UCSC or a custom browser.
+**annotate** Annotate coverage of features from multiple files.
+**bamtobed** Convert BAM alignments to BED (& other) formats.
+**bamtofastq** Convert BAM records to FASTQ records.
+**bed12tobed6** Breaks BED12 intervals into discrete BED6 intervals.
+**bedpetobam** Convert BEDPE intervals to BAM records.
+**bedtobam** Convert intervals to BAM records.
+**closest** Find the closest, potentially non-overlapping interval.
+**cluster** Cluster (but don't merge) overlapping/nearby intervals.
+**complement** Extract intervals _not_ represented by an interval file.
+**coverage** Compute the coverage over defined intervals.
+**expand** Replicate lines based on lists of values in columns.
+**flank** Create new intervals from the flanks of existing intervals.
+**genomecov** Compute the coverage over an entire genome.
+**getfasta** Use intervals to extract sequences from a FASTA file.
+**groupby** Group by common cols. & summarize oth. cols. (~ SQL "groupBy")
+**igv** Create an IGV snapshot batch script.
+**intersect** Find overlapping intervals in various ways.
+**jaccard** Calculate the Jaccard statistic b/w two sets of intervals.
+**links** Create a HTML page of links to UCSC locations.
+**makewindows** Make interval "windows" across a genome.
+**map** Apply a function to a column for each overlapping interval.
+**maskfasta** Use intervals to mask sequences from a FASTA file.
+**merge** Combine overlapping/nearby intervals into a single interval.
+**multicov** Counts coverage from multiple BAMs at specific intervals.
+**multiinter** Identifies common intervals among multiple interval files.
+**nuc** Profile the nucleotide content of intervals in a FASTA file.
+**overlap** Computes the amount of overlap from two intervals.
+**pairtobed** Find pairs that overlap intervals in various ways.
+**pairtopair** Find pairs that overlap other pairs in various ways.
+**random** Generate random intervals in a genome.
+**reldist** Calculate the distribution of relative distances b/w two files.
+**shuffle** Randomly redistrubute intervals in a genome.
+**slop** Adjust the size of intervals.
+**sort** Order the intervals in a file.
+**subtract** Remove intervals based on overlaps b/w two files.
+**tag** Tag BAM alignments based on overlaps with interval files.
+**unionbedg** Combines coverage intervals from multiple BEDGRAPH files.
+**window** Find overlapping intervals within a window around an interval.
=========================== =========================================================================================================================================================
@@ -76,19 +84,19 @@ Utility Description
===========================
-1.3 Fundamental concepts.
+Fundamental concepts.
===========================
------------------------------------------------------
-1.3.1 What are genome features and how are they represented?
+What are genome features and how are they represented?
------------------------------------------------------
-Throughout this manual, we will discuss how to use BEDTools to manipulate, compare and ask questions of genome “features”. Genome features can be functional elements (e.g., genes), genetic polymorphisms (e.g.
+Throughout this manual, we will discuss how to use bedtools to manipulate, compare and ask questions of genome “features”. Genome features can be functional elements (e.g., genes), genetic polymorphisms (e.g.
SNPs, INDELs, or structural variants), or other annotations that have been discovered or curated by genome sequencing groups or genome browser groups. In addition, genome features can be custom annotations that
an individual lab or researcher defines (e.g., my novel gene or variant).
The basic characteristics of a genome feature are the chromosome or scaffold on which the feature “resides”, the base pair on which the
feature starts (i.e. the “start”), the base pair on which feature ends (i.e. the “end”), the strand on which the feature exists (i.e. “+” or “-“), and the name of the feature if one is applicable.
-The two most widely used formats for representing genome features are the BED (Browser Extensible Data) and GFF (General Feature Format) formats. BEDTools was originally written to work exclusively with genome features
+The two most widely used formats for representing genome features are the BED (Browser Extensible Data) and GFF (General Feature Format) formats. bedtools was originally written to work exclusively with genome features
described using the BED format, but it has been recently extended to seamlessly work with BED, GFF and VCF files.
Existing annotations for the genomes of many species can be easily downloaded in BED and GFF
@@ -96,7 +104,7 @@ format from the UCSC Genome Browser’s “Table Browser” (http://genome.ucsc.
Ensemble Genome Browser contains annotations in GFF/GTF format for many species (http://www.ensembl.org/info/data/ftp/index.html)
-------------------------------------
-1.3.2 Overlapping / intersecting features.
+Overlapping / intersecting features.
-------------------------------------
Two genome features (henceforth referred to as “features”) are said to overlap or intersect if they share at least one base in common.
In the figure below, Feature A intersects/overlaps Feature B, but it does not intersect/overlap Feature C.
@@ -104,26 +112,26 @@ In the figure below, Feature A intersects/overlaps Feature B, but it does not in
**TODO: place figure here**
--------------------------------------------
-1.3.3 Comparing features in file “A” and file “B”.
+Comparing features in file “A” and file “B”.
--------------------------------------------
-The previous section briefly introduced a fundamental naming convention used in BEDTools. Specifically, all BEDTools that compare features contained in two distinct files refer to one file as feature set “A” and the other file as feature set “B”. This is mainly in the interest of brevity, but it also has its roots in set theory.
-As an example, if one wanted to look for SNPs (file A) that overlap with exons (file B), one would use intersectBed in the following manner::
+The previous section briefly introduced a fundamental naming convention used in bedtools. Specifically, all bedtools that compare features contained in two distinct files refer to one file as feature set “A” and the other file as feature set “B”. This is mainly in the interest of brevity, but it also has its roots in set theory.
+As an example, if one wanted to look for SNPs (file A) that overlap with exons (file B), one would use bedtools intersect in the following manner::
- intersectBed –a snps.bed –b exons.bed
+ bedtools intersect –a snps.bed –b exons.bed
There are two exceptions to this rule: 1) When the “A” file is in BAM format, the “-abam” option must bed used. For example::
- intersectBed –abam alignedReads.bam –b exons.bed
+ bedtools intersect –abam alignedReads.bam –b exons.bed
And 2) For tools where only one input feature file is needed, the “-i” option is used. For example::
- mergeBed –i repeats.bed
+ bedtools merge –i repeats.bed
-----------------------------------------------------
-1.3.4 BED starts are zero-based and BED ends are one-based.
+BED starts are zero-based and BED ends are one-based.
-----------------------------------------------------
-BEDTools users are sometimes confused by the way the start and end of BED features are represented. Specifically, BEDTools uses the UCSC Genome Browser’s internal database convention of making the start position 0-based and the end position 1-based: (http://genome.ucsc.edu/FAQ/FAQtracks#tracks1)
-In other words, BEDTools interprets the “start” column as being 1 basepair higher than what is represented in the file. For example, the following BED feature represents a single base on chromosome 1; namely, the 1st base::
+bedtools users are sometimes confused by the way the start and end of BED features are represented. Specifically, bedtools uses the UCSC Genome Browser’s internal database convention of making the start position 0-based and the end position 1-based: (http://genome.ucsc.edu/FAQ/FAQtracks#tracks1)
+In other words, bedtools interprets the “start” column as being 1 basepair higher than what is represented in the file. For example, the following BED feature represents a single base on chromosome 1; namely, the 1st base::
chr1 0 1 first_base
@@ -131,27 +139,27 @@ Why, you might ask? The advantage of storing features this way is that when comp
the calculation would be (slightly) more complex (i.e. (end-start)+1). Thus, storing BED features this way reduces the computational burden.
-----------------------------------------------------
-1.3.5 GFF starts and ends are one-based.
+GFF starts and ends are one-based.
-----------------------------------------------------
-In contrast, the GFF format uses 1-based coordinates for both the start and the end positions. BEDTools is aware of this and adjusts the positions accordingly.
-In other words, you don’t need to subtract 1 from the start positions of your GFF features for them to work correctly with BEDTools.
+In contrast, the GFF format uses 1-based coordinates for both the start and the end positions. bedtools is aware of this and adjusts the positions accordingly.
+In other words, you don’t need to subtract 1 from the start positions of your GFF features for them to work correctly with bedtools.
-----------------------------------------------------
-1.3.6 VCF coordinates are one-based.
+VCF coordinates are one-based.
-----------------------------------------------------
-The VCF format uses 1-based coordinates. As in GFF, BEDTools is aware of this and adjusts the positions accordingly.
-In other words, you don’t need to subtract 1 from the start positions of your VCF features for them to work correctly with BEDTools.
+The VCF format uses 1-based coordinates. As in GFF, bedtools is aware of this and adjusts the positions accordingly.
+In other words, you don’t need to subtract 1 from the start positions of your VCF features for them to work correctly with bedtools.
-----------------------------------------------------
-1.3.7 File B is loaded into memory (most of the time).
+File B is loaded into memory (most of the time).
-----------------------------------------------------
-Whenever a BEDTool compares two files of features, the “B” file is loaded into memory. By contrast, the “A” file is processed line by line and compared with the features from B.
+Whenever a bedtool compares two files of features, the “B” file is loaded into memory. By contrast, the “A” file is processed line by line and compared with the features from B.
Therefore to minimize memory usage, one should set the smaller of the two files as the B file. One salient example is the comparison of aligned sequence reads from a
current DNA sequencer to gene annotations. In this case, the aligned sequence file (in BED format) may have tens of millions of features (the sequence alignments),
while the gene annotation file will have tens of thousands of features. In this case, it is wise to sets the reads as file A and the genes as file B.
-----------------------------------------------------
-1.3.8 Feature files *must* be tab-delimited.
+Feature files *must* be tab-delimited.
-----------------------------------------------------
This is rather self-explanatory. While it is possible to allow BED files to be space-delimited, we have decided to require tab delimiters for three reasons:
@@ -160,37 +168,37 @@ This is rather self-explanatory. While it is possible to allow BED files to be s
3. GFF files can contain spaces within attribute columns. This complicates the use of space-delimited files as spaces must therefore be treated specially depending on the context.
-------------------------------------------------------------
-1.3.9 All BEDTools allow features to be “piped” via standard input.
+All bedtools allow features to be “piped” via standard input.
-------------------------------------------------------------
-In an effort to allow one to combine multiple BEDTools and other UNIX utilities into more complicated “pipelines”, all BEDTools allow features
-to be passed to them via standard input. Only one feature file may be passed to a BEDTool via standard input.
-The convention used by all BEDTools is to set either file A or file B to “stdin” or "-". For example::
+In an effort to allow one to combine multiple bedtools and other UNIX utilities into more complicated “pipelines”, all bedtools allow features
+to be passed to them via standard input. Only one feature file may be passed to a bedtool via standard input.
+The convention used by all bedtools is to set either file A or file B to “stdin” or "-". For example::
- cat snps.bed | intersectBed –a stdin –b exons.bed
- cat snps.bed | intersectBed –a - –b exons.bed
+ cat snps.bed | bedtools intersect –a stdin –b exons.bed
+ cat snps.bed | bedtools intersect –a - –b exons.bed
-In addition, all BEDTools that simply require one main input file (the -i file) will assume that input is
+In addition, all bedtools that simply require one main input file (the -i file) will assume that input is
coming from standard input if the -i parameter is ignored. For example, the following are equivalent::
- cat snps.bed | sortBed –i stdin
- cat snps.bed | sortBed
+ cat snps.bed | bedtools sort –i stdin
+ cat snps.bed | bedtools sort
------------------------------------------------------
-1.3.10 Most BEDTools write their results to standard output.
+Most bedtools write their results to standard output.
------------------------------------------------------
-To allow one to combine multiple BEDTools and other UNIX utilities into more complicated “pipelines”,
-most BEDTools report their output to standard output, rather than to a named file. If one wants to write the output to a named file, one can use the UNIX “file redirection” symbol “>” to do so.
+To allow one to combine multiple bedtools and other UNIX utilities into more complicated “pipelines”,
+most bedtools report their output to standard output, rather than to a named file. If one wants to write the output to a named file, one can use the UNIX “file redirection” symbol “>” to do so.
Writing to standard output (the default)::
- intersectBed –a snps.bed –b exons.bed
+ bedtools intersect –a snps.bed –b exons.bed
chr1 100100 100101 rs233454
chr1 200100 200101 rs446788
chr1 300100 300101 rs645678
Writing to a file::
- intersectBed –a snps.bed –b exons.bed > snps.in.exons.bed
+ bedtools intersect –a snps.bed –b exons.bed > snps.in.exons.bed
cat snps.in.exons.bed
chr1 100100 100101 rs233454
@@ -198,12 +206,12 @@ Writing to a file::
chr1 300100 300101 rs645678
------------------------
-1.3.11 What is a “genome” file?
+What is a “genome” file?
------------------------
-Some of the BEDTools (e.g., genomeCoverageBed, complementBed, slopBed) need to know the size of
+Some of the bedtools (e.g., ``genomecov``, ``complement``, ``slop``) need to know the size of
the chromosomes for the organism for which your BED files are based. When using the UCSC Genome
Browser, Ensemble, or Galaxy, you typically indicate which species / genome build you are working.
-The way you do this for BEDTools is to create a “genome” file, which simply lists the names of the
+The way you do this for bedtools is to create a “genome” file, which simply lists the names of the
chromosomes (or scaffolds, etc.) and their size (in basepairs).
Genome files must be tab-delimited and are structured as follows (this is an example for C. elegans)::
@@ -213,13 +221,13 @@ Genome files must be tab-delimited and are structured as follows (this is an exa
chrX 17718854
chrM 13794
-BEDTools includes predefined genome files for human and mouse in the /genomes directory included
-in the BEDTools distribution. Additionally, the “chromInfo” files/tables available from the UCSC
+bedtools includes predefined genome files for human and mouse in the /genomes directory included
+in the bedtools distribution. Additionally, the “chromInfo” files/tables available from the UCSC
Genome Browser website are acceptable. For example, one can download the hg19 chromInfo file here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
------------------------------------
-1.3.12 Paired-end BED files (BEDPE files).
+Paired-end BED files (BEDPE files).
------------------------------------
We have defined a new file format (BEDPE) to concisely describe disjoint genome features, such as
structural variations or paired-end sequence alignments. We chose to define a new format because the
@@ -227,26 +235,26 @@ existing BED block format (i.e. BED12) does not allow inter-chromosomal feature
the BED12 format feels rather bloated when one want to describe events with only two blocks.
------------------------------------------
-1.3.13 Use “-h” for help with any BEDTool.
+Use “-h” for help with any bedtool.
------------------------------------------
-Rather straightforward. If you use the “-h” option with any BEDTool, a full menu of example usage
+Rather straightforward. If you use the “-h” option with any bedtool, a full menu of example usage
and available options (when applicable) will be reported.
--------------------------------------------------
-1.3.14 BED features must not contain negative positions.
+BED features must not contain negative positions.
--------------------------------------------------
-BEDTools will typically reject BED features that contain negative positions. In special cases, however,
+bedtools will typically reject BED features that contain negative positions. In special cases, however,
BEDPE positions may be set to -1 to indicate that one or more ends of a BEDPE feature is unaligned.
---------------------------------------------------
-1.3.15 The start position must be <= to the end position.
+The start position must be <= to the end position.
---------------------------------------------------
-BEDTools will reject BED features where the start position is greater than the end position.
+bedtools will reject BED features where the start position is greater than the end position.
-----------------------------------------
-1.3.16 Headers are allowed in GFF and BED files
+Headers are allowed in GFF and BED files
-----------------------------------------
-BEDTools will ignore headers at the beginning of BED and GFF files. Valid header lines begin with a
+bedtools will ignore headers at the beginning of BED and GFF files. Valid header lines begin with a
“#” symbol, the work “track”, or the word “browser”. For example, the following examples are valid
headers for BED or GFF files::
@@ -263,20 +271,20 @@ headers for BED or GFF files::
chr5 2380000 2386000 read2 60 -
-------------------------------------------------------------
-1.3.17 GZIP support: BED, GFF, VCF, and BEDPE file can be “gzipped”
+GZIP support: BED, GFF, VCF, and BEDPE file can be “gzipped”
-------------------------------------------------------------
-BEDTools will process gzipped BED, GFF, VCF and BEDPE files in the same manner as
+bedtools will process gzipped BED, GFF, VCF and BEDPE files in the same manner as
uncompressed files. Gzipped files are auto-detected thanks to a helpful contribution from Gordon
Assaf.
----------------------------------------------------------------------------
-1.3.18 Support for “split” or “spliced” BAM alignments and “blocked” BED features
+Support for “split” or “spliced” BAM alignments and “blocked” BED features
----------------------------------------------------------------------------
-As of Version 2.8.0, five BEDTools (``intersectBed``, ``coverageBed``, ``genomeCoverageBed``,
+As of Version 2.8.0, five bedtools (``intersect``, ``coverage``, ``genomecob``,
``bamToBed``, and ``bed12ToBed6``) can properly handle “split”/”spliced” BAM alignments (i.e., having an
“N” CIGAR operation) and/or “blocked” BED (aka BED12) features.
-``intersectBed``, ``coverageBed``, and ``genomeCoverageBed`` will optionally handle “split” BAM and/or
+``intersect``, ``coverage``, and ``genomecov`` will optionally handle “split” BAM and/or
“blocked” BED by using the ``-split`` option. This will cause intersects or coverage to be computed only
for the alignment or feature blocks. In contrast, without this option, the intersects/coverage would be
computed for the entire “span” of the alignment or feature, regardless of the size of the gaps between
@@ -293,56 +301,27 @@ be reported for the portions of the read that overlap the exons (i.e. 30bp on on
Using the -split option with bamToBed causes “spliced/split” alignments to be reported in BED12
-format. Using the -split option with bed12ToBed6 causes “blocked” BED12 features to be reported in
+format. Using the -split option with ``bed12tobed6`` causes “blocked” BED12 features to be reported in
BED6 format.
--------------------------------
-1.3.19 Writing uncompressed BAM output.
+Writing uncompressed BAM output.
--------------------------------
When working with a large BAM file using a complex set of tools in a pipe/stream, it is advantageous
to pass uncompressed BAM output to each downstream program. This minimizes the amount of time
-spent compressing and decompressing output from one program to the next. All BEDTools that create
-BAM output (e.g. ``intersectBed``, ``windowBed``) will now optionally create uncompressed BAM output
+spent compressing and decompressing output from one program to the next. All bedtools that create
+BAM output (e.g. ``intersect``, ``window``) will now optionally create uncompressed BAM output
using the ``-ubam`` option.
=====================================
-1.4 Implementation and algorithmic notes.
+Implementation and algorithmic notes.
=====================================
-BEDTools was implemented in C++ and makes extensive use of data structures and fundamental
+bedtools was implemented in C++ and makes extensive use of data structures and fundamental
algorithms from the Standard Template Library (STL). Many of the core algorithms are based upon the
genome binning algorithm described in the original UCSC Genome Browser paper (Kent et al, 2002).
The tools have been designed to inherit core data structures from central source files, thus allowing
rapid tool development and deployment of improvements and corrections. Support for BAM files is
made possible through Derek Barnett’s elegant C++ API called BamTools.
-
-
-=====================================
-1.5 License and availability.
-=====================================
-BEDTools is freely available under a GNU Public License (Version 2) at:
-http://bedtools.googlecode.com
-
-
-
-=====================================
-1.6 Mailing list.
-=====================================
-A discussion group for reporting bugs, asking questions of the developer and of the user community, as
-well as for requesting new features is available at:
-http://groups.google.com/group/bedtools-discuss
-
-
-
-=====================================
-1.7 Contributors.
-=====================================
-As open-source software, BEDTools greatly benefits from contributions made by other developers and
-users of the tools. We encourage and welcome suggestions, contributions and complaints. This is how
-software matures, improves and stays on top of the needs of its user community. The Google Code
-(GC) site maintains a list of individuals who have contributed either source code or useful ideas for
-improving the tools. In the near future, we hope to maintain a source repository on the GC site in
-order to facilitate further contributions. We are currently unable to do so because we use Git for
-version control, which is not yet supported by GC.
\ No newline at end of file
diff --git a/docs/content/pairToBed.rst b/docs/content/pairToBed.rst
deleted file mode 100755
index 75db129..0000000
--- a/docs/content/pairToBed.rst
+++ /dev/null
@@ -1,378 +0,0 @@
-###############
-5.2 pairToBed
-###############
-**pairToBed** compares each end of a BEDPE feature or a paired-end BAM alignment to a feature file in
-search of overlaps.
-
-**NOTE: pairToBed requires that the BAM file is sorted/grouped by the read name. This
-allows pairToBed to extract correct alignment coordinates for each end based on their
-respective CIGAR strings. It also assumes that the alignments for a given pair come in
-groups of twos. There is not yet a standard method for reporting multiple alignments
-using BAM. pairToBed will fail if an aligner does not report alignments in pairs.**
-
-==========================================================================
-5.2.1 Usage and option summary
-==========================================================================
-**Usage:**
-::
- pairToBed [OPTIONS] [-a <BEDPE> || -abam <BAM>] -b <BED/GFF/VCF>
-
-
-=========================== =========================================================================================================================================================
-Option Description
-=========================== =========================================================================================================================================================
-**-a** BEDPE file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe. Output will be in BEDPE format.
-**-b** BED file B. Use "stdin" if passing B with a UNIX pipe.
-**-abam** BAM file A. Each end of each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view �Cb <BAM> | pairToBed �Cabam stdin �Cb genes.bed | samtools view -
-**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
-**-bedpe** When using BAM input (-abam), write output as BEDPE. The default is to write output in BAM when using -abam. For example: pairToBed �Cabam reads.bam �Cb genes.bed �Cbedpe
-**-ed** Use BAM total edit distance (NM tag) for BEDPE score. Default for BEDPE is to use the *minimum* of the two mapping qualities for the pair. When -ed is used the *total* edit distance from the two mates is reported as the score.
-**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-**-s** Force "strandedness". That is, only report hits in B that overlap A on the **same** strand. By default, overlaps are reported without respect to strand.
-**-type**
- Approach to reporting overlaps between BEDPE and BED.
-
-
- **either-** Report overlaps if either end of A overlaps B.
-
- - *Default*
-
- **neither-** Report A if neither end of A overlaps B.
-
- **xor-** Report overlaps if one and only one end of A overlaps B.
-
- **both-** Report overlaps if both ends of A overlap B.
-
- **notboth-** Report overlaps if neither end or one and only one end of A overlap B.
-
- **ispan-** Report overlaps between [end1, start2] of A and B.
-
- - Note: If chrom1 <> chrom2, entry is ignored.
-
- **ospan-** Report overlaps between [start1, end2] of A and B.
-
- - Note: If chrom1 <> chrom2, entry is ignored.
-
- **notispan-** Report A if ispan of A doesn't overlap B.
- - Note: If chrom1 <> chrom2, entry is ignored.
-
- **notospan-** Report A if ospan of A doesn't overlap B.
- - Note: If chrom1 <> chrom2, entry is ignored.
-=========================== =========================================================================================================================================================
-
-
-
-==========================================================================
-5.2.2 Default behavior
-==========================================================================
-By default, a BEDPE / BAM feature will be reported if *either* end overlaps a feature in the BED file.
-In the example below, the left end of the pair overlaps B yet the right end does not. Thus, BEDPE/
-BAM A is reported since the default is to report A if either end overlaps B.
-
-Default: Report A if *either* end overlaps B.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-==========================================================================
-5.2.3 (-type)Optional overlap requirements
-==========================================================================
-Using then **-type** option, **pairToBed** provides several other overlap requirements for controlling how
-overlaps between BEDPE/BAM A and BED B are reported. The examples below illustrate how each
-option behaves.
-
-**-type both**: Report A only if *both* ends overlap B.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-**-type neither**: Report A only if *neither* end overlaps B.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-**-type xor**: Report A only if *one and only one* end overlaps B.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^ ^^^^^^
-
- Result
-
-
-**-type notboth**: Report A only if *neither end* **or** *one and only one* end overlaps B. Thus "notboth"
-includes what would be reported by "neither" and by "xor".
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^ ^^^^^^
-
- Result
-
-
-**-type ispan**: Report A if it's "*inner span*" overlaps B. Applicable only to intra-chromosomal features.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Inner span |-------------------------------|
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^
-
- Result =====.................................=====
-
-
-
- BEDPE/BAM A =====.................................=====
-
- BED File B ====
-
- Result
-
-
-**-type ospan**: Report A if it's "*outer span*" overlaps B. Applicable only to intra-chromosomal features.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Outer span |-----------------------------------------|
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^^^^^
-
- Result =====.................................=====
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^
-
- Result
-
-
-**-type notispan**: Report A only if it's "*inner span*" does not overlap B. Applicable only to intrachromosomal
-features.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Inner span |-------------------------------|
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^
-
- Result
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^
-
- Result =====.................................=====
-
-
-**-type notospan**: Report A if it's "*outer span*" overlaps B. Applicable only to intra-chromosomal
-features.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Outer span |-----------------------------------------|
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^^^^^^^^^
-
- Result
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^
-
- Result =====.................................=====
-
-
-
-==========================================================================
-5.2.4 (-f)Requiring a minimum overlap fraction
-==========================================================================
-By default, **pairToBed** will report an overlap between A and B so long as there is at least one base
-pair is overlapping on either end. Yet sometimes you may want to restrict reported overlaps between A
-and B to cases where the feature in B overlaps at least X% (e.g. 50%) of A. The **�Cf** option does exactly
-this. The **-f** option may also be combined with the -type option for additional control. For example,
-combining **-f 0.50** with **-type both** requires that both ends of A have at least 50% overlap with a
-feature in B.
-
-For example, report A only at least 50% of one of the two ends is overlapped by B.
-::
- pairToBed -a A.bedpe -b B.bed -f 0.5
-
-
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^ ^^^^^^
-
- Result
-
-
-
- BEDPE/BAM A *****.................................*****
-
- BED File B ^^^^ ^^^^^^
-
- Result =====.................................=====
-
-
-
-==========================================================================
-5.2.5 (-s)Enforcing "strandedness"
-==========================================================================
-By default, **pairToBed** will report overlaps between features even if the features are on opposing
-strands. However, if strand information is present in both files and the **"-s"** option is used, overlaps will
-only be reported when features are on the same strand.
-
-For example, report A only at least 50% of one of the two ends is overlapped by B.
-::
- pairToBed -a A.bedpe -b B.bed -s
-
-
-
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BEDPE/BAM A >>>>>.................................<<<<<
-
- BED File B << >>>>>
-
- Result
-
-
-
- BEDPE/BAM A >>>>>.................................<<<<<
-
- BED File B >> >>>>>
-
- Result >>>>>.................................<<<<<
-
-
-==========================================================================
-5.2.6 (-abam)Default is to write BAM output when using BAM input
-==========================================================================
-When comparing *paired* alignments in BAM format (**-abam**) to features in BED format (**-b**),
-**pairToBed** will , by default, write the output in BAM format. That is, each alignment in the BAM
-file that meets the user's criteria will be written (to standard output) in BAM format. This serves as a
-mechanism to create subsets of BAM alignments are of biological interest, etc. Note that both
-alignments for each aligned pair will be written to the BAM output.
-
-For example:
-::
- pairToBed �Cabam pairedReads.bam �Cb simreps.bed | samtools view - | head -4
-
- JOBU_0001:3:1:4:1060#0 99 chr10 42387928 29 50M = 42393091 5 2 1 3
- AA A A A C G G A A T T A T C G A A T G G A A T C G A A G A G A A T C T T C G A A C G G A C C C G A
- dcgggggfbgfgdgggggggfdfgggcggggfcggcggggggagfgbggc XT:A:R NM:i:5 SM:i:0 AM:i:0 X0:i:3 X 1 : i :
- 3 XM:i:5 XO:i:0 XG:i:0 MD:Z:0T0C33A5T4T3
- JOBU_0001:3:1:4:1060#0 147 chr10 42393091 0 50M = 42387928 - 5 2 1 3
- AAATGGAATCGAATGGAATCAACATCAAATGGAATCAAATGGAATCATTG K g d c g g d e c d g
- \d`ggfcgcggffcgggc^cgfgccgggfc^gcdgg\bg XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:3 X1:i:13 XM:i:2 X O : i :
- 0 XG:i:0 MD:Z:21T14G13
- JOBU_0001:3:1:8:446#0 99 chr10 42388091 9 50M = 42392738 4 6 9 7
- GAATCGACTGGAATCATCATCGGATGGAAATGAATGGAATAATCATCGAA f _ O f f ` ] I e Y f f ` f f e d d c f e f c P ` c _ W \ \ R _ ]
- _BBBBBBBBBBBBBBBB XT:A:U NM:i:4 SM:i:0 AM:i:0 X0:i:1 X1:i:3 XM:i:4 XO:i:0 XG:i:0 M D : Z :
- 7A22C9C2T6
- JOBU_0001:3:1:8:446#0 147 chr10 42392738 9 50M = 42388091 - 4 6 9 7
- TTATCGAATGCAATCGAATGGAATTATCGAATGCAATCGAATAGAATCAT df^ffec_JW[`MWceRec``fee`dcecfeeZae`c]
- f^cNeecfccf^ XT:A:R NM:i:1 SM:i:0 AM:i:0 X0:i:2 X1:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:38A11
-
-
-
-==========================================================================
-5.2.7 (-bedpe)Output BEDPE format when using BAM input
-==========================================================================
-When comparing *paired* alignments in BAM format (**-abam**) to features in BED format (**-b**),
-**pairToBed** will optionally write the output in BEDPE format. That is, each alignment in the BAM
-file is converted to a 10 column BEDPE feature and if overlaps are found (or not) based on the user's
-criteria, the BAM alignment will be reported in BEDPE format. The BEDPE "name" field is comprised
-of the RNAME field in the BAM alignment. The "score" field is the mapping quality score from the
-BAM alignment.
-
-For example:
-::
- pairToBed �Cabam pairedReads.bam �Cb simreps.bed -bedpe | head -5
- chr10 42387927 42387977 chr10 42393090 42393140
- JOBU_0001:3:1:4:1060#0 29 + -
- chr10 42388090 42388140 chr10 42392737 42392787
- JOBU_0001:3:1:8:446#0 9 + -
- chr10 42390552 42390602 chr10 42396045 42396095
- JOBU_0001:3:1:10:1865#0 9 + -
- chrX 139153741 139153791 chrX 139159018 139159068
- JOBU_0001:3:1:14:225#0 37 + -
- chr4 9236903 9236953 chr4 9242032 9242082
- JOBU_0001:3:1:15:1362#0 0 + -
diff --git a/docs/content/quick-start.rst b/docs/content/quick-start.rst
index 64f2df3..5bb3e4a 100755
--- a/docs/content/quick-start.rst
+++ b/docs/content/quick-start.rst
@@ -3,58 +3,71 @@ Quick start
###########
================
-Install BEDTools
+Install bedtools
================
-::
+
+.. code-block:: bash
curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
tar -zxvf BEDTools.tar.gz
cd BEDTools
- make clean
- make all
+ make
sudo cp bin/* /usr/local/bin/
+
===============
-Use BEDTools
+Use bedtools
===============
-Below are examples of typical BEDTools usage. **Additional usage examples are described in
-section 6 of this manual.** Using the "-h" option with any BEDTools will report a list of all command
-line options.
+Below are examples of typical bedtools usage. Using the "-h" option with any
+bedtools will report a list of all command line options.
+
+
+Report the base-pair overlap between the features in two BED files.
+
+.. code-block:: bash
+
+ bedtools intersect -a reads.bed -b genes.bed
+
-A. Report the base-pair overlap between the features in two BED files.
-::
+Report those entries in A that overlap NO entries in B. Like "grep -v"
- intersectBed -a reads.bed -b genes.bed
+.. code-block:: bash
-B. Report those entries in A that overlap NO entries in B. Like "grep -v"
-::
+ bedtools intersect -a reads.bed -b genes.bed -v
- intersectBed -a reads.bed -b genes.bed �Cv
-C. Read BED A from stdin. Useful for stringing together commands. For example, find genes that overlap LINEs
-but not SINEs.
-::
+Read BED A from STDIN. Useful for stringing together commands. For example,
+find genes that overlap LINEs but not SINEs.
- intersectBed -a genes.bed -b LINES.bed | intersectBed -a stdin -b SINEs.bed �Cv
+.. code-block:: bash
-D. Find the closest ALU to each gene.
-::
+ bedtools intersect -a genes.bed -b LINES.bed | \
+ bedtools intersect -a stdin -b SINEs.bed -v
- closestBed -a genes.bed -b ALUs.bed
+
+Find the closest ALU to each gene.
+
+.. code-block:: bash
+
+ bedtools closest -a genes.bed -b ALUs.bed
-E. Merge overlapping repetitive elements into a single entry, returning the number of entries merged.
-::
- mergeBed -i repeatMasker.bed -n
+Merge overlapping repetitive elements into a single entry, returning the number of entries merged.
+
+.. code-block:: bash
+
+ bedtools merge -i repeatMasker.bed -n
-F. Merge nearby repetitive elements into a single entry, so long as they are within 1000 bp of one another.
-::
- mergeBed -i repeatMasker.bed -d 1000
+Merge nearby repetitive elements into a single entry, so long as they are within 1000 bp of one another.
+
+.. code-block:: bash
+
+ bedtools merge -i repeatMasker.bed -d 1000
-
\ No newline at end of file
+
diff --git a/docs/content/related-tools.rst b/docs/content/related-tools.rst
new file mode 100644
index 0000000..12951bf
--- /dev/null
+++ b/docs/content/related-tools.rst
@@ -0,0 +1,67 @@
+##################
+Related software
+##################
+
+Bedtools has been used as an engine behind other genomics software and has been
+integrated into widely used tools such as Galaxy and IGV. Below is a likely
+incomplete list. If you know of others, please let us know, or better yet,
+edit the document on GitHub and send us a pull request. You can do this by
+clicking on the "Edit and improve this document" link in the lower lefthand
+corner.
+
+
+-------------------
+IGV
+-------------------
+Bedtools is now integrated into the IGV genome viewer as of IGV version 2.2. We
+are actively working withe IGV development team to improve and expand this
+integration. See
+`here <http://www.broadinstitute.org/igv/IGV2.2.x>`_
+and
+`here <https://www.broadinstitute.org/software/igv/bedtools>`_ for details.
+
+ .. image:: images/bedtoolsMenu.png
+
+-------------------
+Galaxy
+-------------------
+
+`Galaxy <https://main.g2.bx.psu.edu/>`_ has its own tools for working with
+genomic intervals under the "Operate on Genomic Intervals" section. A subset
+of complementary Bedtools utilities have also been made available on Galaxy in
+an effort to provide functionality that isn't available with the native Galaxy
+tools.
+
+ .. image:: images/galaxy-bedtools.png
+
+
+-------------------
+Pybedtools
+-------------------
+
+`Pybedtools <http://pypi.python.org/pypi/pybedtools>`_ is a really fantastic
+Python library that wraps (and extends upon) the bedtools utilities and exposes
+them for easy use and new tool development using Python. Pybedtools is actively
+maintained by Ryan Dale.
+
+
+-------------------
+MISO
+-------------------
+
+`MISO <http://genes.mit.edu/burgelab/miso/>`_ is "a probabilistic framework
+that quantitates the expression level of alternatively spliced genes from
+RNA-Seq data, and identifies differentially regulated isoforms or exons across
+samples." A subset of the functionality in MISO depends upon ``bedtools``. MISO
+is developed by Yarden Katz.
+
+
+-------------------
+RetroSeq
+-------------------
+
+`RetroSeq <http://bioinformatics.oxfordjournals.org/content/early/2012/12/10/bioinformatics.bts697.abstract>`_
+is "a tool for discovery and genotyping of transposable element variants (TEVs)
+(also known as mobile element insertions) from next-gen sequencing reads aligned
+to a reference genome in BAM format". RetroSeq is developed by Thomas Keane.
+Source code can be obtained on `GitHub <https://github.com/tk2/RetroSeq>`_.
\ No newline at end of file
diff --git a/docs/content/shuffleBed.rst b/docs/content/shuffleBed.rst
deleted file mode 100755
index d840277..0000000
--- a/docs/content/shuffleBed.rst
+++ /dev/null
@@ -1,155 +0,0 @@
-###############
-5.13 shuffleBed
-###############
-**shuffleBed** will randomly permute the genomic locations of a fearure file among a genome defined in a
-genome file. One can also provide an "exclusions" BED/GFF/VCF file that lists regions where you do
-not want the permuted features to be placed. For example, one might want to prevent features from
-being placed in known genome gaps. **shuffleBed** is useful as a *null* basis against which to test the
-significance of associations of one feature with another.
-
-
-
-==========================================================================
-5.13.1 Usage and option summary
-==========================================================================
-Usage:
-::
- shuffleBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-excl** A BED file of coordinates in which features from -i should *not* be placed (e.g., genome gaps).
-**-chrom** Keep features in -i on the same chromosome. Solely permute their location on the chromosome. *By default, both the chromosome and position are randomly chosen*.
-**-seed** Supply an integer seed for the shuffling. This will allow feature shuffling experiments to be recreated exactly as the seed for the pseudo-random number generation will be constant. *By default, the seed is chosen automatically*.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-
-==========================================================================
-5.13.2 Default behavior
-==========================================================================
-By default, **shuffleBed** will reposition each feature in the input BED file on a random chromosome at a
-random position. The size and strand of each feature are preserved.
-
-For example:
-::
- cat A.bed
- chr1 0 100 a1 1 +
- chr1 0 1000 a2 2 -
-
- cat my.genome
- chr1 10000
- chr2 8000
- chr3 5000
- chr4 2000
-
- shuffleBed -i A.bed -g my.genome
- chr4 1498 1598 a1 1 +
- chr3 2156 3156 a2 2 -
-
-
-
-
-
-==========================================================================
-5.13.3 (-chrom)Requiring that features be shuffled on the same chromosome
-==========================================================================
-The "**-chrom**" option behaves the same as the default behavior except that features are randomly
-placed on the same chromosome as defined in the BED file.
-
-For example:
-::
- cat A.bed
- chr1 0 100 a1 1 +
- chr1 0 1000 a2 2 -
-
- cat my.genome
- chr1 10000
- chr2 8000
- chr3 5000
- chr4 2000
-
- shuffleBed -i A.bed -g my.genome -chrom
- chr1 9560 9660 a1 1 +
- chr1 7258 8258 a2 2 -
-
-
-
-
-==========================================================================
-5.13.4 Excluding certain genome regions from shuffleBed
-==========================================================================
-One may want to prevent BED features from being placed in certain regions of the genome. For
-example, one may want to exclude genome gaps from permutation experiment. The "**-excl**" option
-defines a BED file of regions that should be excluded. **shuffleBed** will attempt to permute the
-locations of all features while adhering to the exclusion rules. However it will stop looking for an
-appropriate location if it cannot find a valid spot for a feature after 1,000,000 tries.
-
-For example (*note that the exclude file excludes all but 100 base pairs of the chromosome*):
-::
- cat A.bed
- chr1 0 100 a1 1 +
- chr1 0 1000 a2 2 -
-
- cat my.genome
- chr1 10000
-
- cat exclude.bed
- chr1 100 10000
-
- shuffleBed -i A.bed -g my.genome -excl exclude.bed
- chr1 0 100 a1 1 +
- Error, line 2: tried 1000000 potential loci for entry, but could not avoid excluded
- regions. Ignoring entry and moving on.
-
-
-For example (*now the exclusion file only excludes the first 100 bases of the chromosome*):
-::
- cat A.bed
- chr1 0 100 a1 1 +
- chr1 0 1000 a2 2 -
-
- cat my.genome
- chr1 10000
-
- cat exclude.bed
- chr1 0 100
-
- shuffleBed -i A.bed -g my.genome -excl exclude.bed
- chr1 147 247 a1 1 +
- chr1 2441 3441 a2 2 -
-
-
-==========================================================================
-5.13.5 Defining a "seed" for the random replacement.
-==========================================================================
-**shuffleBed** uses a pseudo-random number generator to permute the locations of BED features.
-Therefore, each run should produce a different result. This can be problematic if one wants to exactly
-recreate an experiment. By using the "**-seed**" option, one can supply a custom integer seed for
-**shuffleBed**. In turn, each execution of **shuffleBed** with the same seed and input files should produce
-identical results.
-
-For example (*note that the exclude file below excludes all but 100 base pairs of the chromosome*):
-::
- cat A.bed
- chr1 0 100 a1 1 +
- chr1 0 1000 a2 2 -
-
- cat my.genome
- chr1 10000
-
- shuffleBed -i A.bed -g my.genome -seed 927442958
- chr1 6177 6277 a1 1 +
- chr1 8119 9119 a2 2 -
-
- shuffleBed -i A.bed -g my.genome -seed 927442958
- chr1 6177 6277 a1 1 +
- chr1 8119 9119 a2 2 -
-
- . . .
-
- shuffleBed -i A.bed -g my.genome -seed 927442958
- chr1 6177 6277 a1 1 +
- chr1 8119 9119 a2 2 -
diff --git a/docs/content/slopBed.rst b/docs/content/slopBed.rst
deleted file mode 100755
index 0646afc..0000000
--- a/docs/content/slopBed.rst
+++ /dev/null
@@ -1,84 +0,0 @@
-###############
-5.14 slopBed
-###############
-**slopBed** will increase the size of each feature in a feature file be a user-defined number of bases. While
-something like this could be done with an "**awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'**",
-**slopBed** will restrict the resizing to the size of the chromosome (i.e. no start < 0 and no end >
-chromosome size).
-
-
-==========================================================================
-5.14.1 Usage and option summary
-==========================================================================
-Usage:
-::
- slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
-
-=========================== ===============================================================================================================================================================================================================
- Option Description
-=========================== ===============================================================================================================================================================================================================
-**-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.
-**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
-**-r** The number of base pairs to add to the end coordinate. *Integer*.
-**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-==========================================================================
-5.14.2 Default behavior
-==========================================================================
-By default, **slopBed** will either add a fixed number of bases in each direction (**-b**) or an asymmetric
-number of bases in each direction (**-l** and **-r**).
-
-For example:
-::
- cat A.bed
- chr1 5 100
- chr1 800 980
-
- cat my.genome
- chr1 1000
-
- slopBed -i A.bed -g my.genome -b 5
- chr1 0 105
- chr1 795 985
-
- slopBed -i A.bed -g my.genome -l 2 -r 3
- chr1 3 103
- chr1 798 983
-
-
-However, if the requested number of bases exceeds the boundaries of the chromosome, **slopBed** will
-"clip" the feature accordingly.
-::
- cat A.bed
- chr1 5 100
- chr1 800 980
-
- cat my.genome
- chr1 1000
-
- slopBed -i A.bed -g my.genome -b 5000
- chr1 0 1000
- chr1 0 1000
-
-
-
-==========================================================================
-5.14.3 Resizing features according to strand
-==========================================================================
-**slopBed** will optionally increase the size of a feature based on strand.
-
-For example:
-::
- cat A.bed
- chr1 100 200 a1 1 +
- chr1 100 200 a2 2 -
-
- cat my.genome
- chr1 1000
-
- slopBed -i A.bed -g my.genome -l 50 -r 80 -s
- chr1 50 280 a1 1 +
- chr1 20 250 a2 2 -
diff --git a/docs/content/subtractBed.rst b/docs/content/subtractBed.rst
deleted file mode 100755
index 81dfb0e..0000000
--- a/docs/content/subtractBed.rst
+++ /dev/null
@@ -1,88 +0,0 @@
-###############
-5.7 subtractBed
-###############
-**subtractBed** searches for features in B that overlap A. If an overlapping feature is found in B, the
-overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B
-overlaps all of a feature in A, the A feature will not be reported.
-
-
-==========================================================================
-5.7.1 Usage and option summary
-==========================================================================
-Usage:
-::
- subtractBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
-
-=========================== ===============================================================================================================================================================================================================
-Option Description
-=========================== ===============================================================================================================================================================================================================
-**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
-**-s** Force strandedness. That is, find the closest feature in B overlaps A on the same strand. *By default, this is disabled*.
-=========================== ===============================================================================================================================================================================================================
-
-
-
-==========================================================================
-5.7.2 Default behavior
-==========================================================================
-Figure:
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- BED FILE A ************* ******
-
- BED File B ^^^^^^^^ ^^^^^^^^^^^
-
- Result =========
-
-For example:
-::
- cat A.bed
- chr1 100 200
- chr1 10 20
-
- cat B.bed
- chr1 0 30
- chr1 180 300
-
- subtractBed -a A.bed -b B.bed
- chr1 100 180
-
-
-
-
-
-
-==========================================================================
-5.7.3 (-f)Requiring a minimal overlap fraction before subtracting
-==========================================================================
-This option behaves the same as the -f option for intersectBed. In this case, subtractBed will only
-subtract an overlap with B if it covers at least the fraction of A defined by -f. If an overlap is found,
-but it does not meet the overlap fraction, the original A feature is reported without subtraction.
-
-For example:
-::
- cat A.bed
- chr1 100 200
-
- cat B.bed
- chr1 180 300
-
- subtractBed -a A.bed -b B.bed -f 0.10
- chr1 100 180
-
- subtractBed -a A.bed -b B.bed -f 0.80
- chr1 100 200
-
-
-
-
-==========================================================================
-5.7.4 (-s)Enforcing "strandedness"
-==========================================================================
-This option behaves the same as the -s option for intersectBed while scanning for features in B that
-should be subtracted from A. See the discussion in the intersectBed section for details.
-
-
-
-
diff --git a/docs/content/tips-and-tricks.rst b/docs/content/tips-and-tricks.rst
new file mode 100644
index 0000000..61f3598
--- /dev/null
+++ b/docs/content/tips-and-tricks.rst
@@ -0,0 +1,7 @@
+###############
+Tips and Tricks
+###############
+
+======================
+The ``-sorted`` option
+======================
\ No newline at end of file
diff --git a/docs/content/tools/annotate.rst b/docs/content/tools/annotate.rst
new file mode 100755
index 0000000..3345a7d
--- /dev/null
+++ b/docs/content/tools/annotate.rst
@@ -0,0 +1,120 @@
+.. _annotate:
+
+###############
+*annotate*
+###############
+``bedtools annotate``, well, annotates one BED/VCF/GFF file with the coverage
+and number of overlaps observed from multiple other BED/VCF/GFF files.
+In this way, it allows one to ask to what degree one feature coincides with
+multiple other feature types with a single command.
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools annotate [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
+
+**(or)**:
+::
+
+ annotateBed [OPTIONS] -i <BED/GFF/VCF> -files FILE1 FILE2 FILE3 ... FILEn
+
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-names** A list of names (one per file) to describe each file in -i. These names will be printed as a header line.
+**-counts** Report the count of features in each file that overlap -i. Default behavior is to report the fraction of -i covered by each file.
+**-both** Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file.
+**-s** Force strandedness. That is, only include hits in A that overlap B on the same strand. By default, hits are included without respect to strand.
+**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
+=========================== ===============================================================================================================================================================================================================
+
+==========================================================================
+Default behavior - annotate one file with coverage from others.
+==========================================================================
+By default, the fraction of each feature covered by each annotation file is
+reported after the complete feature in the file to be annotated.
+
+.. code-block:: bash
+
+ $ cat variants.bed
+ chr1 100 200 nasty 1 -
+ chr2 500 1000 ugly 2 +
+ chr3 1000 5000 big 3 -
+
+ $ cat genes.bed
+ chr1 150 200 geneA 1 +
+ chr1 175 250 geneB 2 +
+ chr3 0 10000 geneC 3 -
+
+ $ cat conserve.bed
+ chr1 0 10000 cons1 1 +
+ chr2 700 10000 cons2 2 -
+ chr3 4000 10000 cons3 3 +
+
+ $ cat known_var.bed
+ chr1 0 120 known1 -
+ chr1 150 160 known2 -
+ chr2 0 10000 known3 +
+
+ $ bedtools annotate -i variants.bed -files genes.bed conserve.bed known_var.bed
+ chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
+ chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
+ chr3 1000 5000 big 3 - 1.000000 0.250000 0.000000
+
+
+==========================================================================
+``-count`` Report the count of hits from the annotation files
+==========================================================================
+
+.. code-block:: bash
+
+ $ bedtools annotate -counts -i variants.bed -files genes.bed conserve.bed known_var.bed
+ chr1 100 200 nasty 1 - 2 1 2
+ chr2 500 1000 ugly 2 + 0 1 1
+ chr3 1000 5000 big 3 - 1 1 0
+
+
+
+===========================================================================================
+``-both`` Report both the count of hits and the fraction covered from the annotation files
+===========================================================================================
+
+.. code-block:: bash
+
+ $ bedtools annotate -both -i variants.bed -files genes.bed conserve.bed known_var.bed
+ #chr start end name score +/- cnt1 pct1 cnt2 pct2 cnt3 pct3
+ chr1 100 200 nasty 1 - 2 0.500000 1 1.000000 2 0.300000
+ chr2 500 1000 ugly 2 + 0 0.000000 1 0.600000 1 1.000000
+ chr3 1000 5000 big 3 - 1 1.000000 1 0.250000 0 0.000000
+
+
+
+
+==========================================================================
+``-s`` Restrict the reporting to overlaps on the **same** strand.
+==========================================================================
+
+.. code-block:: bash
+
+ $ bedtools annotate -s -i variants.bed -files genes.bed conserve.bed known_var.bed
+ chr1 100 200 nasty 1 - 0.000000 0.000000 0.000000
+ chr2 500 1000 ugly 2 + 0.000000 0.000000 0.000000
+ chr3 1000 5000 big 3 - 1.000000 0.000000 0.000000
+
+
+
+==========================================================================
+``-S`` Restrict the reporting to overlaps on the **opposite** strand.
+==========================================================================
+
+.. code-block:: bash
+
+ $ bedtools annotate -S -i variants.bed -files genes.bed conserve.bed known_var.bed
+ chr1 100 200 nasty 1 - 0.500000 1.000000 0.300000
+ chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000
+ chr3 1000 5000 big 3 - 0.000000 0.250000 0.000000
+
diff --git a/docs/content/tools/bamtobed.rst b/docs/content/tools/bamtobed.rst
new file mode 100755
index 0000000..2cb22f8
--- /dev/null
+++ b/docs/content/tools/bamtobed.rst
@@ -0,0 +1,159 @@
+.. _bamtobed:
+
+###############
+*bamtobed*
+###############
+``bedtools bamtobed`` is a conversion utility that converts sequence alignments
+in BAM format into BED, BED12, and/or BEDPE records.
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools bamtobed [OPTIONS] -i <BAM>
+
+**(or)**:
+::
+
+ bamToBed [OPTIONS] -i <BAM>
+
+
+
+.. tabularcolumns:: |p{4.5cm}|p{8.5cm}|
+
+============= ================================================================
+Option Description
+============= ================================================================
+**-bedpe** Write BAM alignments in BEDPE format. Only one alignment from
+ paired-end reads will be reported. Specifically, it each mate
+ is aligned to the same chromosome, the BAM alignment reported
+ will be the one where the BAM insert size is greater than zero.
+ When the mate alignments are interchromosomal, the
+ lexicographically lower chromosome will be reported first.
+ Lastly, when an end is unmapped, the chromosome and strand will
+ be set to "." and the start and end coordinates will be set
+ to -1. *By default, this is disabled and the output will be
+ reported in BED format*.
+**-mate1** When writing BEDPE (-bedpe) format,
+ always report mate one as the first BEDPE "block".
+**-bed12** Write "blocked" BED (a.k.a. BED12) format. This will convert
+ "spliced" BAM alignments (denoted by the "N" CIGAR operation)
+ to BED12. `Forces -split`.
+**-split** Report each portion of a "split" BAM (i.e., having an "N" CIGAR
+ operation) alignment as a distinct BED intervals.
+**-splitD** Report each portion of a "split" BAM while obeying noth "N" CIGAR
+ and "D" operation. Forces `-split`.
+**-ed** Use the "edit distance" tag (NM) for the BED score field.
+ Default for BED is to use mapping quality. Default for BEDPE is
+ to use the *minimum* of the two mapping qualities for the pair.
+ When -ed is used with -bedpe, the total edit distance from the
+ two mates is reported.
+**-tag** Use other *numeric* BAM alignment tag for BED score. Default
+ for BED is to use mapping quality. Disallowed with BEDPE output.
+**-color** An R,G,B string for the color used with BED12 format. Default
+ is (255,0,0).
+**-cigar** Add the CIGAR string to the BED entry as a 7th column.
+============= ================================================================
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, each alignment in the BAM file is converted to a 6 column BED. The
+BED "name" field is comprised of the RNAME field in the BAM alignment. If mate
+information is available, the mate (e.g., "/1" or "/2") field will be appended
+to the name.
+
+.. code-block:: bash
+
+ $ bedtools bamtobed -i reads.bam | head -3
+ chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 37 -
+ chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 37 +
+ chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 37 -
+
+
+==========================================================================
+``-tag`` Set the score field based on BAM tags
+==========================================================================
+One can override the choice of the BAM `MAPQ` as the result BED record's `score`
+field by using the ``-tag`` option. In the example below, we use the ``-tag``
+option to select the BAM edit distance (the `NM` tag) as the score
+column in the resulting BED records.
+
+.. code-block:: bash
+
+ $ bedtools bamtobed -i reads.bam -tag NM | head -3
+ chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 1 -
+ chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 3 +
+ chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 1 -
+
+
+==========================================================================
+``-bedpe`` Set the score field based on BAM tags
+==========================================================================
+The ``-bedpe`` option converts BAM alignments to BEDPE format, thus allowing
+the two ends of a paired-end alignment to be reported on a single text line.
+Specifically, it each mate is aligned to the same chromosome,
+the BAM alignment reported will be the one where the BAM insert size is greater
+than zero. When the mate alignments are interchromosomal, the lexicographically
+lower chromosome will be reported first. Lastly, when an end is unmapped, the
+chromosome and strand will be set to "." and the start and end coordinates will
+be set to -1.
+
+.. note::
+
+ When using this option, it is required that the BAM
+ file is sorted/grouped by the read name. This allows bamToBed
+ to extract correct alignment coordinates for each end based on
+ their respective CIGAR strings. It also assumes that the
+ alignments for a given pair come in groups of twos. There is
+ not yet a standard method for reporting multiple alignments
+ using BAM. bamToBed will fail if an aligner does not report
+ alignments in pairs.
+
+.. code-block:: bash
+
+ $ bedtools bamtobed -i reads.ba -bedpe | head -3
+ chr7 118965072 118965122 chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0 37 + -
+ chr11 46765606 46765656 chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0 37 + -
+ chr20 54704674 54704724 chr20 54708987 54709037 TUPAC_0001:3:1:1:1833#0 37 +
+
+
+One can easily use samtools and bamToBed together as part of a UNIX pipe. In
+this example, we will only convert properly-paired (``FLAG == 0x2``) reads to
+BED format.
+
+.. code-block:: bash
+
+ $ samtools view -bf 0x2 reads.bam | bedtools bamtobed -i stdin | head
+ chr7 118970079 118970129 TUPAC_0001:3:1:0:1452#0/1 37 -
+ chr7 118965072 118965122 TUPAC_0001:3:1:0:1452#0/2 37 +
+ chr11 46769934 46769984 TUPAC_0001:3:1:0:1472#0/1 37 -
+ chr11 46765606 46765656 TUPAC_0001:3:1:0:1472#0/2 37 +
+ chr20 54704674 54704724 TUPAC_0001:3:1:1:1833#0/1 37 +
+ chr20 54708987 54709037 TUPAC_0001:3:1:1:1833#0/2 37 -
+ chrX 9380413 9380463 TUPAC_0001:3:1:1:285#0/1 0 -
+ chrX 9375861 9375911 TUPAC_0001:3:1:1:285#0/2 0 +
+ chrX 131756978 131757028 TUPAC_0001:3:1:2:523#0/1 37 +
+ chrX 131761790 131761840 TUPAC_0001:3:1:2:523#0/2 37 -
+
+
+==================================================================
+``-split`` Creating BED12 features from "spliced" BAM entries.
+==================================================================
+``bedtools bamtobed`` will, by default, create a BED6 feature that represents
+the entire span of a spliced/split BAM alignment. However, when using the
+``-split`` command, a BED12 feature is reported where BED blocks will be
+created for each aligned portion of the sequencing read.
+
+::
+ Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ Exons *************** **********
+
+ BED/BAM A ^^^^^^^^^^^^....................................^^^^
+
+ Result =============== ====
+
diff --git a/docs/content/tools/bamtofastq.rst b/docs/content/tools/bamtofastq.rst
new file mode 100644
index 0000000..217d678
--- /dev/null
+++ b/docs/content/tools/bamtofastq.rst
@@ -0,0 +1,103 @@
+.. _bamtofastq:
+
+###############
+*bamtofastq*
+###############
+``bedtools bamtofastq`` is a conversion utility for extracting FASTQ records
+from sequence alignments in BAM format.
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools bamtofastq [OPTIONS] -i <BAM> -fq <FASTQ>
+
+**(or)**:
+::
+
+ bamToFastq [OPTIONS] -i <BAM> -fq <FASTQ>
+
+
+
+.. tabularcolumns:: |p{4.5cm}|p{8.5cm}|
+
+============= ================================================================
+Option Description
+============= ================================================================
+**-fq2** FASTQ for second end. Used if BAM contains paired-end data.
+ BAM should be sorted by query name
+ (``samtools sort -n aln.bam aln.qsort``) if creating
+ paired FASTQ with this option.
+**-tags** Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
+============= ================================================================
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, each alignment in the BAM file is converted to a FASTQ record
+in the ``-fq`` file. The order of the records in the resulting FASTQ exactly
+follows the order of the records in the BAM input file.
+
+.. code-block:: bash
+
+ $ bedtools bamtofastq -i NA18152.bam -fq NA18152.fq
+
+ $ head -8 NA18152.fq
+ @NA18152-SRR007381.35051
+ GGAGACATATCATATAAGTAATGCTAGGGTGAGTGGTAGGAAGTTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGTGACAAAATATGTTGTATAGAGTTCAGGGGAGAGTGCGTCATATGTTGTTCCTAGGAAGATTGTAGTGGTGAGGGTGTTTATTATAATAATGTTTGTGTATTCGGCTATGAAGAATAGGGCGAAGGGGCCTGCGGCGTATTCGATGTTGAAGCCTGAGACTAGTTCGGACTCCCCTTCGGCAAGGTCGAA
+ +
+ <<<;;<;<;;<;;;;;;;;;;;;<<<:;;;;;;;;;;;;;;;;::::::;;;;<<;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<<;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<;;;;;:;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<;;;;;;;;;;<<<<<<<<;;;;;;;;;:;;;;;;;;;;;;;;;;;;;:;;;;8;;8888;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;8966689666666299866669:899
+ @NA18152-SRR007381.637219
+ AATGCTAGGGTGAGTGGTAGGAAGTTTTTTCATAGGAGGTGTATGAGTTGGTCGTAGCGGAATCGGGGGTATGCTGTTCGAATTCATAAGAACAGGGAGGTTAGAAGTAGGGTCTTGGTGACAAAATATGTTGTATAGAGTTCAGGGGAGAGTGCGTCATATGTTGTTCCTAGGAAGATTGTAGTGGTGAGGGTGTTTATTATAATAATGTTTGTGTATTCGGCTATGAAGAATAGGGCGAAGGGGCCTGCGGCGTATTCGATGTTGAAGCCTGAGACTAGTTCGGACTCCCCTTCCGGCAAGGTCGAA
+ +
+ <<<<<<<<<<;;<;<;;;;<<;<888888899<;;;;;;<;;;;;;;;;;;;;;;;;;;;;;;;<<<<<;;;;;;;;;<;<<<<<;;;;;;;;;;;;;<<<<;;;;;;;:::;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<<<<;;;;;;;;;;;;;;;;;;;;;;;<;;;;;;;;;;;;;;;;;;;;;;<888<;<<;;;;<<<<<<;;;;;<<<<<<<<;;;;;;;;;:;;;;888888899:::;;8;;;;;;;;;;;;;;;;;;;99;;99666896666966666600;96666669966
+
+
+
+==========================================================================
+``-fq2`` Creating two FASTQ files for paired-end sequences.
+==========================================================================
+If your BAM alignments are from paired-end sequence data, one can use the
+``-fq2`` option to create two distinct FASTQ output files --- one for
+end 1 and one for end 2.
+
+.. note::
+
+ When using this option, it is required that the BAM
+ file is sorted/grouped by the read name. This keeps the resulting records
+ in the two output FASTQ files in the same order. One can sort the BAM
+ file by query name with ``samtools sort -n aln.bam aln.qsort``.
+
+
+.. code-block:: bash
+
+ $ samtools sort -n aln.bam aln.qsort
+
+ $ bedtools bamtofastq -i aln.qsort.bam \
+ -fq aln.end1.fq \
+ -fq2 aln.end2.fq
+
+ $ head -8 aln.end1.fq
+ @SRR069529.2276/1
+ CAGGGAGAAGGAGGTAGGAAAGAGAAAGGACCAGGGAGGGGCGCATACACAGGACGCTCCGTGCGGTGATAGCAGCACCACACTGTGTTCAGTCGTCTGGC
+ +
+ =;@>==###############################################################################################
+ @SRR069529.2406/1
+ GCTGGGAAAAGGATTCAGGATGTTGGTTTCTATCTTTGAGTTGCTGCTGTGCGGCTGTCCCTACACTCGCAGTACCCCTCGGACACCGTCTACTGTGGAGG
+ +
+ =5@><<:?<?
+
+ $ head -8 aln.end2.fq
+ @SRR069529.2276/2
+ AGACCCAGAGAGGGACAGGATCTGTCCCAGATCATAAAATAGGGGGAGTGCTCCGTAGAGGCGTGCGCGGTGGCACCGTGCAGTAGTACGGGTGAGCGGGG
+ +
+ #####################################################################################################
+ @SRR069529.2406/2
+ TTCCCTACCCCTGGGGTCAGGGACTACAGCCAAGGGGAGAACTTTAGCAAGTAGACGTTAGTTATTTTGATTCCAGTGGGGACGCGCGTGTAGCGAGTTGT
+ +
+ @>=AABB?AAACABBA>@?AAAA>B@@AB at AA:B at AA@??#############################################################
+
+
diff --git a/docs/content/bed12ToBed6.rst b/docs/content/tools/bed12tobed6.rst
similarity index 90%
rename from docs/content/bed12ToBed6.rst
rename to docs/content/tools/bed12tobed6.rst
index d9159e3..e29105b 100755
--- a/docs/content/bed12ToBed6.rst
+++ b/docs/content/tools/bed12tobed6.rst
@@ -1,5 +1,7 @@
+.. _bed12tobed6:
+
###############
-5.21 bed12ToBed6
+*bed12tobed6*
###############
**bed12ToBed6** is a convenience tool that converts BED features in BED12 (a.k.a. "blocked" BED
features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons,
@@ -7,9 +9,10 @@ bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).
==========================================================================
-5.21.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
bed12ToBed6 [OPTIONS] -i <BED12>
@@ -23,17 +26,15 @@ Usage:
==========================================================================
-5.21.2 Default behavior
+Default behavior
==========================================================================
Figure:
+
::
head data/knownGene.hg18.chr21.bed | tail -n 3
- chr21 10079666 10120808 uc002yiv.1 0 - 10081686 1 0 1 2 0 6 0 8
- 0 4 528,91,101,215, 0,1930,39750,40927,
- chr21 10080031 10081687 uc002yiw.1 0 - 10080031 1 0 0 8 0 0 3 1
- 0 2 200,91, 0,1565,
- chr21 10081660 10120796 uc002yix.2 0 - 10081660 1 0 0 8 1 6 6 0
- 0 3 27,101,223,0,37756,38913,
+ chr21 10079666 10120808 uc002yiv.1 0 - 10081686 1 0 1 2 0 6 0 8 0 4 528,91,101,215, 0,1930,39750,40927,
+ chr21 10080031 10081687 uc002yiw.1 0 - 10080031 1 0 0 8 0 0 3 1 0 2 200,91, 0,1565,
+ chr21 10081660 10120796 uc002yix.2 0 - 10081660 1 0 0 8 1 6 6 0 0 3 27,101,223,0,37756,38913,
head data/knownGene.hg18.chr21.bed | tail -n 3 | bed12ToBed6 -i stdin
chr21 10079666 10080194 uc002yiv.1 0 -
diff --git a/docs/content/tools/bedpetobam.rst b/docs/content/tools/bedpetobam.rst
new file mode 100644
index 0000000..92151b6
--- /dev/null
+++ b/docs/content/tools/bedpetobam.rst
@@ -0,0 +1,5 @@
+.. _bedpetobam:
+
+###############
+*bedpetobam*
+###############
diff --git a/docs/content/bedToBam.rst b/docs/content/tools/bedtobam.rst
similarity index 96%
rename from docs/content/bedToBam.rst
rename to docs/content/tools/bedtobam.rst
index c0f1d6a..3177dd0 100755
--- a/docs/content/bedToBam.rst
+++ b/docs/content/tools/bedtobam.rst
@@ -1,13 +1,16 @@
+.. _bedtobam:
+
###############
-5.18 bedToBam
+*bedtobam*
###############
**bedToBam** converts features in a feature file to BAM format. This is useful as an efficient means of
storing large genome annotations in a compact, indexed format for visualization purposes.
==========================================================================
-5.18.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
bedToBam [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> > <BAM>
@@ -23,9 +26,10 @@ Usage:
==========================================================================
-5.18.2 Default behavior
+Default behavior
==========================================================================
The default behavior is to assume that the input file is in unblocked format. For example:
+
::
head -5 rmsk.hg18.chr21.bed
chr21 9719768 9721892 ALR/Alpha 1004 +
@@ -45,7 +49,7 @@ The default behavior is to assume that the input file is in unblocked format. Fo
==========================================================================
-5.18.3 Creating "spliced" BAM entries from "blocked" BED features
+Creating "spliced" BAM entries from "blocked" BED features
==========================================================================
Optionally, **bedToBam** will create spliced BAM entries from "blocked" BED features by using the
-bed12 option. This will create CIGAR strings in the BAM output that will be displayed as "spliced"
@@ -53,6 +57,7 @@ alignments. The image illustrates this behavior, as the top track is a BAM repre
bedToBam) of a BED file of UCSC genes.
For example:
+
::
bedToBam -i knownGene.hg18.chr21.bed -g human.hg18.genome -bed12 > knownGene.bam
diff --git a/docs/content/closestBed.rst b/docs/content/tools/closest.rst
similarity index 96%
rename from docs/content/closestBed.rst
rename to docs/content/tools/closest.rst
index 3276718..aa13756 100755
--- a/docs/content/closestBed.rst
+++ b/docs/content/tools/closest.rst
@@ -1,5 +1,7 @@
+.. _closest:
+
###############
-5.6 closestBed
+*closest*
###############
Similar to **intersectBed, closestBed** searches for overlapping features in A and B. In the event that
no feature in B overlaps the current feature in A, **closestBed** will report the *closest* (that is, least
@@ -11,6 +13,7 @@ overlapping feature as the closest---that is, it does not restrict to closest *n
5.6.1 Usage and option summary
==========================================================================
**Usage:**
+
::
closestBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
@@ -35,12 +38,13 @@ Option Description
==========================================================================
-5.6.2 Default behavior
+Default behavior
==========================================================================
**closestBed** first searches for features in B that overlap a feature in A. If overlaps are found, the feature
in B that overlaps the highest fraction of A is reported. If no overlaps are found, **closestBed** looks for
the feature in B that is *closest* (that is, least genomic distance to the start or end of A) to A. For
example, in the figure below, feature B1 would be reported as the closest feature to A1.
+
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -52,6 +56,7 @@ example, in the figure below, feature B1 would be reported as the closest featur
For example:
+
::
cat A.bed
chr1 100 200
@@ -66,7 +71,7 @@ For example:
==========================================================================
-5.6.3 (-s)Enforcing "strandedness"
+``-s`` Enforcing "strandedness"
==========================================================================
This option behaves the same as the -s option for intersectBed while scanning for the closest
(overlapping or not) feature in B. See the discussion in the intersectBed section for details.
@@ -74,7 +79,7 @@ This option behaves the same as the -s option for intersectBed while scanning fo
==========================================================================
-5.6.4 (-t)Controlling how ties for "closest" are broken
+``-t`` Controlling how ties for "closest" are broken
==========================================================================
When there are two or more features in B that overlap the *same fraction* of A, **closestBed** will, by
default, report both features in B. Imagine feature A is a SNP and file B contains genes. It can often
@@ -84,6 +89,7 @@ choose the just first or last feature (in terms of where it occurred in the inpu
position) that occurred in B.
For example (note the difference between -l 200 and -l 300):
+
::
cat A.bed
chr1 100 101 rs1234
@@ -112,10 +118,11 @@ For example (note the difference between -l 200 and -l 300):
==========================================================================
-5.6.5 (-d)Reporting the distance to the closest feature in base pairs
+``-d`` Reporting the distance to the closest feature in base pairs
==========================================================================
ClosestBed will optionally report the distance to the closest feature in the B file using the **-d** option.
When a feature in B overlaps a feature in A, a distance of 0 is reported.
+
::
cat A.bed
chr1 100 200
diff --git a/docs/content/tools/cluster.rst b/docs/content/tools/cluster.rst
new file mode 100644
index 0000000..90a5c8b
--- /dev/null
+++ b/docs/content/tools/cluster.rst
@@ -0,0 +1,123 @@
+.. _cluster:
+
+###############
+*cluster*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/cluster-glyph.png
+ :width: 600pt
+|
+
+
+Similar to :doc:`../tools/merge`, ``cluster`` report each set of overlapping or
+"book-ended" features in an interval file. In contrast to ``merge``,
+``cluster`` does not flatten the cluster of intervals into a new meta-interval;
+instead, it assigns an unique cluster ID to each record in each cluster. This
+is useful for having fine control over how sets of overlapping intervals in
+a single interval file are combined.
+
+.. note::
+
+ ``bedtools cluster`` requires that you presort your data by chromosome and
+ then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
+ for BED files).
+
+.. seealso::
+
+ :doc:`../tools/merge`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools cluster [OPTIONS] -i <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ clusterBed [OPTIONS] -i <BED/GFF/VCF>
+
+
+
+=========================== ===============================================================================================================================================================================================================
+Option Description
+=========================== ===============================================================================================================================================================================================================
+**-s** Force strandedness. That is, only cluster features that are the same strand. *By default, this is disabled*.
+**-d** Maximum distance between features allowed for features to be clustered. *Default is 0. That is, overlapping and/or book-ended features are clustered*.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools cluster`` collects overlapping (by at least 1 bp) and/or
+bookended intervals into distinct clusters. In the example below, the 4th
+column is the cluster ID.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 180 250
+ chr1 250 500
+ chr1 501 1000
+
+ $ bedtools cluster -i A.bed
+ chr1 100 200 1
+ chr1 180 250 1
+ chr1 250 500 1
+ chr1 501 1000 2
+
+
+==========================================================================
+``-s`` Enforcing "strandedness"
+==========================================================================
+The ``-s`` option will only cluster intervals that are overlapping/bookended
+*and* are on the same strand.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+ chr1 180 250 a2 2 +
+ chr1 250 500 a3 3 -
+ chr1 501 1000 a4 4 +
+
+ $ bedtools cluster -i A.bed -s
+ chr1 100 200 a1 1 + 1
+ chr1 180 250 a2 2 + 1
+ chr1 501 1000 a4 4 + 2
+ chr1 250 500 a3 3 - 3
+
+
+==========================================================================
+``-d`` Controlling how close two features must be in order to cluster
+==========================================================================
+By default, only overlapping or book-ended features are combined into a new
+feature. However, one can force ``cluster`` to combine more distant features
+with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
+features that overlap or are within 1000 base pairs of one another will be
+clustered.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 501 1000
+
+ $ bedtools cluster -i A.bed
+ chr1 100 200 1
+ chr1 501 1000 2
+
+ $ bedtools cluster -i A.bed -d 1000
+ chr1 100 200 1
+ chr1 501 1000 1
+
diff --git a/docs/content/tools/complement.rst b/docs/content/tools/complement.rst
new file mode 100755
index 0000000..a3c850f
--- /dev/null
+++ b/docs/content/tools/complement.rst
@@ -0,0 +1,62 @@
+.. _complement:
+
+###############
+*complement*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/complement-glyph.png
+ :width: 600pt
+
+|
+
+
+``bedtools complement`` returns all intervals in a genome that are **not**
+covered by at least one interval in the input BED/GFF/VCF file.
+
+
+.. seealso::
+
+ :doc:`../tools/merge`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools complement -i <BED/GFF/VCF> -g <GENOME>
+
+**(or)**:
+::
+
+ complementBed -i <BED/GFF/VCF> -g <GENOME>
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools complement`` returns all genomic intervals that are not
+covered by at least one record from the input file.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 400 500
+ chr1 500 800
+
+ $ cat my.genome
+ chr1 1000
+ chr2 800
+
+ $ bedtools complement -i A.bed -g my.genome
+ chr1 0 100
+ chr1 200 400
+ chr1 800 1000
+ chr2 0 800
+
+
+
diff --git a/docs/content/coverageBed.rst b/docs/content/tools/coverage.rst
similarity index 94%
rename from docs/content/coverageBed.rst
rename to docs/content/tools/coverage.rst
index ccd5acd..f5de907 100755
--- a/docs/content/coverageBed.rst
+++ b/docs/content/tools/coverage.rst
@@ -1,5 +1,7 @@
+.. _coverage:
+
###############
-5.9 coverageBed
+*coverage*
###############
**coverageBed** computes both the *depth* and *breadth* of coverage of features in file A across the features
in file B. For example, **coverageBed** can compute the coverage of sequence alignments (file A) across 1
@@ -9,9 +11,10 @@ computes the fraction of bases in B interval that were overlapped by one or more
**coverageBed** also computes the *breadth* of coverage for each interval in B.
==========================================================================
-5.9.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
coverageBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
@@ -41,7 +44,7 @@ Option Description
==========================================================================
-5.9.2 Default behavior
+Default behavior
==========================================================================
After each interval in B, **coverageBed** will report:
@@ -51,6 +54,7 @@ After each interval in B, **coverageBed** will report:
4) The fraction of bases in B that had non-zero coverage from features in A.
Below are the number of features in A (N=...) overlapping B and fraction of bases in B with coverage.
+
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -59,10 +63,11 @@ Below are the number of features in A (N=...) overlapping B and fraction of base
BED File A ^^^^ ^^^^ ^^ ^^^^^^^^^ ^^^ ^^ ^^^^
^^^^^^^^ ^^^^^ ^^^^^ ^^
- Result [ N=3, 10/15 ] [ N=1, 2/16 ] [N=1,6/6] [N=5, 11/12 ]
+ Result [ N=3, 10/15 ] [ N=1, 2/15 ] [N=1,6/6] [N=6, 12/14 ]
For example:
+
::
cat A.bed
chr1 10 20
@@ -83,12 +88,13 @@ For example:
==========================================================================
-5.9.4 (-s)Calculating coverage by strand
+``-s`` Calculating coverage by strand
==========================================================================
Use the "**-s**" option if one wants to only count coverage if features in A are on the same strand as the
feature / window in B. This is especially useful for RNA-seq experiments.
For example (note the difference in coverage with and without **-s**:
+
::
cat A.bed
chr1 10 20 a1 1 -
@@ -112,7 +118,7 @@ For example (note the difference in coverage with and without **-s**:
chr2 0 100 b3 1 + 0 0 100 0.0000000
==========================================================================
-5.9.5 (-hist)Creating a histogram of coverage for each feature in the B file
+``-hist`` Creating a histogram of coverage for each feature in the B file
==========================================================================
One should use the "**-hist**" option to create, for each interval in B, a histogram of coverage of the
features in A across B.
@@ -120,6 +126,7 @@ features in A across B.
In this case, each entire feature in B will be reported, followed by the depth of coverage, the number of
bases at that depth, the size of the feature, and the fraction covered. After all of the features in B have
been reported, a histogram summarizing the coverage among all features in B will be reported.
+
::
cat A.bed
chr1 10 20 a1 1 -
@@ -142,14 +149,15 @@ been reported, a histogram summarizing the coverage among all features in B will
-==========================================================================
-5.9.6 (-hist)Reporting the per-base of coverage for each feature in the B file
-==========================================================================
+===========================================================================
+``-d`` Reporting the per-base of coverage for each feature in the B file
+===========================================================================
One should use the "**-d**" option to create, for each interval in B, a detailed list of coverage at each of the
positions across each B interval.
The output will consist of a line for each one-based position in each B feature, followed by the coverage
detected at that position.
+
::
cat A.bed
chr1 0 5
@@ -174,9 +182,9 @@ detected at that position.
-==========================================================================
-5.9.7 (-split)Reporting coverage with spliced alignments or blocked BED features
-==========================================================================
+=============================================================================
+``-split`` Reporting coverage with spliced alignments or blocked BED features
+=============================================================================
As described in section 1.3.19, coverageBed will, by default, screen for overlaps against the entire span
of a spliced/split BAM alignment or blocked BED12 feature. When dealing with RNA-seq reads, for
example, one typically wants to only tabulate coverage for the portions of the reads that come from
diff --git a/docs/content/tools/expand.rst b/docs/content/tools/expand.rst
new file mode 100644
index 0000000..15b53f6
--- /dev/null
+++ b/docs/content/tools/expand.rst
@@ -0,0 +1,5 @@
+.. _expand:
+
+###############
+*expand*
+###############
diff --git a/docs/content/tools/flank.rst b/docs/content/tools/flank.rst
new file mode 100644
index 0000000..db3b9da
--- /dev/null
+++ b/docs/content/tools/flank.rst
@@ -0,0 +1,131 @@
+.. _flank:
+
+###############
+*flank*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/flank-glyph.png
+ :width: 600pt
+
+|
+
+``bedtools flank`` will create two new flanking intervals for each interval in
+a BED/GFF/VCF file. Note that ``flank`` will restrict the created flanking
+intervals to the size of the chromosome (i.e. no start < 0 and no end >
+chromosome size).
+
+.. note::
+
+ In order to prevent creating intervals that violate chromosome boundaries,
+ ``bedtools flank`` requires a *genome* file defining the length of each
+ chromosome or contig.
+
+.. seealso::
+
+ :doc:`../tools/slop`
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools flank [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+**(or):**
+::
+
+ flankBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.
+**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
+**-r** The number of base pairs to add to the end coordinate. *Integer*.
+**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
+**-pct** Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools flank`` will either add a fixed number of bases in each
+direction (``-b``) or an asymmetric number of bases in each direction
+with ``-l`` and ``-r``.
+
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 500 600
+
+ $ cat my.genome
+ chr1 1000
+
+ $ bedtools flank -i A.bed -g my.genome -b 5
+ chr1 95 100
+ chr1 200 205
+ chr1 495 500
+ chr1 600 605
+
+ $ bedtools flank -i A.bed -g my.genome -l 2 -r 3
+ chr1 98 100
+ chr1 200 203
+ chr1 498 500
+ chr1 600 603
+
+
+
+
+However, if the requested number of bases exceeds the boundaries of the
+chromosome, ``bedtools flank`` will "clip" the feature accordingly.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 500 600
+
+ $ cat my.genome
+ chr1 1000
+
+ $ bedtools flank -i A.bed -g my.genome -b 800
+ chr1 0 100
+ chr1 200 1000
+ chr1 0 500
+ chr1 600 1000
+
+
+==========================================================================
+``-pct`` Resizing features by a given fraction
+==========================================================================
+``bedtools flank`` will optionally create flanking intervals whose size is
+user-specified fraction of the original interval.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 500 700
+
+ ################################################################
+ # note the flanking intervals from the second record in A.bed
+ # are 20bp whereas the flanking intervals from the first record
+ # are only 10bp
+ ################################################################
+ $ bedtools flank -i A.bed -g my.genome -b 0.1 -pct
+ chr1 90 100
+ chr1 200 210
+ chr1 480 500
+ chr1 700 720
+
+
+
diff --git a/docs/content/tools/genomecov.rst b/docs/content/tools/genomecov.rst
new file mode 100755
index 0000000..e5fd055
--- /dev/null
+++ b/docs/content/tools/genomecov.rst
@@ -0,0 +1,338 @@
+.. _genomecov:
+
+###############
+*genomecov*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/genomecov-glyph.png
+ :width: 600pt
+
+|
+
+``bedtools genomecov`` computes histograms (default), per-base reports (``-d``)
+and BEDGRAPH (``-bg``) summaries of feature coverage (e.g., aligned sequences)
+for a given genome.
+
+.. note::
+
+ 1. If using BED/GFF/VCF, the input (``-i``) file must be grouped by
+ chromosome. A simple ``sort -k 1,1 in.bed > in.sorted.bed`` will suffice.
+ Also, if using BED/GFF/VCF, one must provide a genome file via the ``-g``
+ argument.
+
+ 2. If the input is in BAM (-ibam) format, the BAM file must be sorted
+ by position. Using ``samtools sort aln.bam aln.sorted`` will suffice.
+
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools genomecov [OPTIONS] [-i|-ibam] -g (iff. -i)
+
+**(or)**:
+::
+
+ genomeCoverageBed [OPTIONS] [-i|-ibam] -g (iff. -i)
+
+
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-ibam** | BAM file as input for coverage. Each BAM alignment in A added to the total coverage for the genome.
+ | Use "stdin" or simply "-" if passing it with a UNIX pipe: For example:
+ | ``samtools view -b <BAM> | genomeCoverageBed -ibam stdin -g hg18.genome``
+**-d** Report the depth at each genome position with 1-based coordinates.
+**-dz** Report the depth at each genome position with 0-based coordinates.
+**-bg** Report depth in BedGraph format. For details, see: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
+**-bga** Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: "grep -w 0$" to the output.
+**-split** Treat "split" BAM or BED12 entries as distinct BED intervals when computing coverage. For BAM files, this uses the CIGAR "N" and "D" operations to infer the blocks for computing coverage. For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12).
+**-strand** Calculate coverage of intervals from a specific strand. With BED files, requires at least 6 columns (strand is column 6).
+**-5** Calculate coverage of 5' positions (instead of entire interval).
+**-3** Calculate coverage of 3' positions (instead of entire interval).
+**-max** Combine all positions with a depth >= max into a single bin in the histogram.
+**-scale** | Scale the coverage by a constant factor.
+ | Each coverage value is multiplied by this factor before being reported.
+ | Useful for normalizing coverage by, e.g., reads per million (RPM).
+ | ``Default is 1.0; i.e., unscaled.``
+**-trackline** | Adds a UCSC/Genome-Browser track line definition in the first line of the output.
+ | See `here <http://genome.ucsc.edu/goldenPath/help/bedgraph.html>`_ for more details about track line definition:
+**-trackopts** Writes additional track line definition parameters in the first line.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools genomecov`` will compute a histogram of coverage for
+the genome file provided. The default output format is as follows:
+
+1. chromosome (or entire genome)
+2. depth of coverage from features in input file
+3. number of bases on chromosome (or genome) with depth equal to column 2.
+4. size of chromosome (or entire genome) in base pairs
+5. fraction of bases on chromosome (or entire genome) with depth equal to column 2.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 20 30
+ chr2 0 500
+
+ $ cat my.genome
+ chr1 1000
+ chr2 500
+
+ $ bedtools genomecov -i A.bed -g my.genome
+ chr1 0 980 1000 0.98
+ chr1 1 20 1000 0.02
+ chr2 1 500 500 1
+ genome 0 980 1500 0.653333
+ genome 1 520 1500 0.346667
+
+
+==========================================================================
+``-max`` Controlling the histogram's maximum depth
+==========================================================================
+Using the ``-max`` option, ``bedtools genomecov`` will "lump" all positions in
+the genome having feature coverage greater than or equal to ``-max`` into
+the ``-max`` histogram bin. For example, if one sets ``-max``
+equal to 50, the max depth reported in the output will be 50 and all positions
+with a depth >= 50 will be represented in bin 50.
+
+
+==========================================================================
+``-d`` Reporting "per-base" genome coverage
+==========================================================================
+Using the ``-d`` option, ``bedtools genomecov`` will compute the depth of
+feature coverage for each base on each chromosome in genome file provided.
+
+The "per-base" output format is as follows:
+
+1. chromosome
+2. chromosome position
+3. depth (number) of features overlapping this chromosome position.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 20 30
+ chr2 0 500
+
+ $ cat my.genome
+ chr1 1000
+ chr2 500
+
+ $ bedtools genomecov -i A.bed -g my.genome -d | \
+ head -15 | \
+ tail -n 10
+ chr1 6 0
+ chr1 7 0
+ chr1 8 0
+ chr1 9 0
+ chr1 10 0
+ chr1 11 1
+ chr1 12 1
+ chr1 13 1
+ chr1 14 1
+ chr1 15 1
+
+
+==========================================================================
+``-bg`` Reporting genome coverage in BEDGRAPH format.
+==========================================================================
+Whereas the ``-d`` option reports an output line describing the observed
+coverage at each and every position in the genome, the ``-bg`` option instead
+produces genome-wide coverage output in
+`BEDGRAPH <http://genome.ucsc.edu/goldenPath/help/bedgraph.html>`_ format.
+This is a much more concise representation since consecutive positions with the
+same coverage are reported as a single output line describing the start and end
+coordinate of the interval having the coverage level, followed by the coverage
+level itself.
+
+
+For example, below is a snippet of BEDGRAPH output of the coverage from a 1000
+Genome Project BAM file:
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg | head
+ chr1 554304 554309 5
+ chr1 554309 554313 6
+ chr1 554313 554314 1
+ chr1 554315 554316 6
+ chr1 554316 554317 5
+ chr1 554317 554318 1
+ chr1 554318 554319 2
+ chr1 554319 554321 6
+ chr1 554321 554323 1
+ chr1 554323 554334 7
+
+Using this format, one can quickly identify regions of the genome with
+sufficient coverage (in this case, 10 or more reads) by piping the
+output to an ``awk`` filter.
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg | \
+ awk '$4 > 9' | \
+ head
+ chr1 554377 554381 11
+ chr1 554381 554385 12
+ chr1 554385 554392 16
+ chr1 554392 554408 17
+ chr1 554408 554410 19
+ chr1 554410 554422 20
+ chr1 554422 554423 19
+ chr1 554423 554430 22
+ chr1 554430 554440 24
+ chr1 554440 554443 25
+
+
+==========================================================================
+``-bga`` Reporting genome coverage for *all* positions in BEDGRAPH format.
+==========================================================================
+The ``-bg`` option reports coverage in BEDGRAPH format only for those regions
+of the genome that actually have coverage. But what about the uncovered portion
+of the genome? By using the ``-bga`` option, one receives a complete report
+including the regions with zero coverage.
+
+For example, compare the output from ``-bg``:
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg | head
+ chr1 554304 554309 5
+ chr1 554309 554313 6
+ chr1 554313 554314 1
+ chr1 554315 554316 6
+ chr1 554316 554317 5
+ chr1 554317 554318 1
+ chr1 554318 554319 2
+ chr1 554319 554321 6
+ chr1 554321 554323 1
+ chr1 554323 554334 7
+
+to the output from ``-bga``:
+
+.. code-block:: bash
+
+ # Note the first record reports that the first 554304
+ # base pairs of chr1 had zero coverage
+ $ bedtools genomecov -ibam NA18152.bam -bga | head
+ chr1 0 554304 0
+ chr1 554304 554309 5
+ chr1 554309 554313 6
+ chr1 554313 554314 1
+ chr1 554314 554315 0
+ chr1 554315 554316 6
+ chr1 554316 554317 5
+ chr1 554317 554318 1
+ chr1 554318 554319 2
+ chr1 554319 554321 6
+
+
+==========================================================================
+``-strand`` Reporting genome coverage for a specific strand.
+==========================================================================
+Whereas the default is to count coverage regardless of strand, the ``-strand``
+option allows one to report the coverage observed for a specific strand.
+
+Compare:
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg | head
+ chr1 554304 554309 5
+ chr1 554309 554313 6
+ chr1 554313 554314 1
+ chr1 554315 554316 6
+ chr1 554316 554317 5
+ chr1 554317 554318 1
+ chr1 554318 554319 2
+ chr1 554319 554321 6
+ chr1 554321 554323 1
+ chr1 554323 554334 7
+
+to
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg -strand + | head
+ chr1 554385 554392 4
+ chr1 554392 554408 5
+ chr1 554408 554430 6
+ chr1 554430 554451 7
+ chr1 554451 554455 8
+ chr1 554455 554490 9
+ chr1 554490 554495 10
+ chr1 554495 554496 9
+ chr1 554496 554574 10
+ chr1 554574 554579 11
+
+
+==========================================================================
+``-scale`` Scaling coverage by a constant factor.
+==========================================================================
+The ``-strand`` option allows one to scale the coverage observed in an interval
+file by a constant factor. Each coverage value is multiplied by this factor
+before being reported. This can be useful for normalizing coverage by,
+e.g., metrics such as reads per million (RPM).
+
+Compare:
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg | head
+ chr1 554304 554309 5
+ chr1 554309 554313 6
+ chr1 554313 554314 1
+ chr1 554315 554316 6
+ chr1 554316 554317 5
+ chr1 554317 554318 1
+ chr1 554318 554319 2
+ chr1 554319 554321 6
+ chr1 554321 554323 1
+ chr1 554323 554334 7
+
+to
+
+.. code-block:: bash
+
+ $ bedtools genomecov -ibam NA18152.bam -bg -scale 10.0 | head
+ chr1 554304 554309 50
+ chr1 554309 554313 60
+ chr1 554313 554314 10
+ chr1 554315 554316 60
+ chr1 554316 554317 50
+ chr1 554317 554318 10
+ chr1 554318 554319 20
+ chr1 554319 554321 60
+ chr1 554321 554323 10
+ chr1 554323 554334 70
+
+
+==============================================================================
+``-split`` Reporting coverage with spliced alignments or blocked BED features
+==============================================================================
+``bedtools genomecov`` will, by default, screen for overlaps against the
+entire span of a spliced/split BAM alignment or blocked BED12 feature. When
+dealing with RNA-seq reads, for example, one typically wants to only screen
+for overlaps for the portions of the reads that come from exons (and ignore the
+interstitial intron sequence). The ``-split`` command allows for such
+overlaps to be performed.
+
+
diff --git a/docs/content/tools/getfasta.rst b/docs/content/tools/getfasta.rst
new file mode 100755
index 0000000..7c65ceb
--- /dev/null
+++ b/docs/content/tools/getfasta.rst
@@ -0,0 +1,252 @@
+.. _getfasta:
+
+###############
+*getfasta*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/getfasta-glyph.png
+ :width: 600pt
+
+
+``bedtools getfasta`` extracts sequences from a FASTA file for each of the
+intervals defined in a BED/GFF/VCF file.
+
+.. tip::
+
+ 1. The headers in the input FASTA file must *exactly* match the chromosome
+ column in the BED file.
+
+ 2. You can use the UNIX ``fold`` command to set the line width of the
+ FASTA output. For example, ``fold -w 60`` will make each line of the FASTA
+ file have at most 60 nucleotides for easy viewing.
+
+.. seealso::
+
+ :doc:`../tools/maskfasta`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**
+
+.. code-block:: bash
+
+ $ bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
+
+**(or):**
+
+.. code-block:: bash
+
+ $ getFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
+
+
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-name** Use the "name" column in the BED file for the FASTA headers in the output FASTA file.
+**-tab** Report extract sequences in a tab-delimited format instead of in FASTA format.
+**-s** Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented. *Default: strand information is ignored*.
+**-split** Given BED12 input, extract and concatenate the sequences from the BED "blocks" (e.g., exons)
+=========================== ===============================================================================================================================================================================================================
+
+
+==========================================================================
+Default behavior
+==========================================================================
+``bedtools getfasta`` will extract the sequence defined by the coordinates
+in a BED interval and create a new FASTA entry in the output file for each
+extracted sequence. By default, the FASTA header for each
+extracted sequence will be formatted as follows: "<chrom>:<start>-<end>".
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10
+
+ $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out
+
+ $ cat test.fa.out
+ >chr1:5-10
+ AAACC
+
+
+
+
+==========================================================================
+``-name`` Using the BED "name" column as a FASTA header.
+==========================================================================
+Using the ``-name`` option, one can set the FASTA header for each extracted
+sequence to be the "name" columns from the BED feature.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10 myseq
+
+ $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out -name
+
+ $ cat test.fa.out
+ >myseq
+ AAACC
+
+
+
+==========================================================================
+``-tab`` Creating a tab-delimited output file in lieu of FASTA output.
+==========================================================================
+Using the ``-tab`` option, the ``-fo`` output file will be tab-delimited
+instead of in FASTA format.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10 myseq
+
+ $ bedtools getfasta -fi test.fa -bed test.bed -fo test.fa.out.tab -name -tab
+
+ $ cat test.fa.out
+ myseq AAACC
+
+
+
+==========================================================================
+``-s`` Forcing the extracted sequence to reflect the requested strand
+==========================================================================
+``bedtools getfasta`` will extract the sequence in the orientation defined in
+the strand column when the "-s" option is used.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 20 25 forward 1 +
+ chr1 20 25 reverse 1 -
+
+ $ bedtools getfasta -fi test.fa -bed test.bed -s -name -fo test.fa.out
+
+ $ cat test.fa.out
+ >forward
+ CGCTA
+ >reverse
+ TAGCG
+
+
+==========================================================================
+``-split`` Extracting BED "blocks".
+==========================================================================
+One can optionally request that FASTA records be extracting and concatenating
+each block in a BED12 record. For example, consider a BED12 record describing a
+transcript. By default, ``getfasta`` will extract the sequence representing the
+entire transcript (intons, exons, UTRs). Using the -split option, ``getfasta``
+will instead produce separate a FASTA record representing a transcript that
+splices together each BED12 block (e.g., exons
+and UTRs in the case of genes described with BED12).
+
+.. code-block:: bash
+
+ $ cat genes.bed12
+ chr1 164404 173864 ENST00000466557.1 0 - 173864 173864 0 6 387,59,66,216,132,112, 0,1479,3695,4644,8152,9348,
+ chr1 235855 267253 ENST00000424587.1 0 - 267253 267253 0 4 2100,150,105,158, 0,2562,23161,31240,
+ chr1 317810 328455 ENST00000426316.1 0 + 328455 328455 0 2 323,145, 0,10500,
+
+ $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name -fo stdout
+ >ENST00000466557.1
+ gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggagttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattagcctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatttcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagcctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGGGAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCACCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTTCACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTTACGTAGATCA [...]
+ >ENST00000424587.1
+ ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggattacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGGCTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGTAAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTCTGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTTTATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGGGTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGTTTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATTTGAAGCAAGT [...]
+ >ENST00000426316.1
+ AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgagagaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtatgagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGCAAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTTTGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTTGTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTTCCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATATTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA
+
+ # use the UNIX fold command to wrap the FASTA sequence such that each line
+ # has at most 60 characters
+ $ bedtools getfasta -fi chr1.fa -bed genes.bed12 -split -name -fo stdout | \
+ fold -w 60
+ >ENST00000466557.1
+ gaggcgggaagatcacttgatatcaggagtcgaggcgggaagatcacttgacgtcaggag
+ ttcgagactggcccggccaacatggtgaaaccgcatctccactaaaaatacaaaaattag
+ cctggtatggtggtgggcacctgtaatcccagtgacttgggaggctaaggcaggagaatt
+ tcttgaacccaggaggcagaggttgcagtgaccagcaaggttgcgccattgcaccccagc
+ ctgggcgataagagtgaaaactccatctcaaaaaaaaaaaaaaaaaaaaaaTTCCTTTGG
+ GAAGGCCTTCTACATAAAAATCTTCAACATGAGACTGGAAAAAAGGGTATGGGATCATCA
+ CCGGACCTTTGGCTTTTACAGCTCGAGCTGACAAAGTTGATTTATCAAGTTGTAAATCTT
+ CACCTGTTGAATTCATAAGTTCATGTCATATTTTCTTTCAGACAATTCTTCAGTTTGTTT
+ ACGTAGATCAGCGATACGATGATTCCATTTCTtcggatccttgtaagagcagagcaggtg
+ atggagagggtgggaggtgtagtgacagaagcaggaaactccagtcattcgagacgggca
+ gcacaagctgcggagtgcaggccacctctacggccaggaaacggattctcccgcagagcc
+ tcggaagctaccgaccctgctcccaccttgactcagtaggacttactgtagaattctggc
+ cttcagacCTGAGCCTGGCAGCTCTCTCCAACTTTGGAAGCCCAGGGGCATGGCCCCTGT
+ CCACAGATGCACCTGGCATGAGGCGTGCCCAGAGGGACAGAGGCAGATGAGTttcgtctc
+ ctccactggattgtgagggcCAGAGTTGAACTCCCTCATTTTCCGTTCCCCAGCATTGGC
+ AGGTTCTGGGACTGGTGGCTGTGGTGGCTCGTTGGTCTTTGTCTCTTAGAAGGTGGGGAA
+ TAATCATCATCT
+ >ENST00000424587.1
+ ccaggaagtgaaaatgacactttactgttttaatttgcatttctctgcttacaagtggat
+ tacacacattttcgtgtgctgttggctacttatTCATTCAGAAAACATACTAAGTGCTGG
+ CTCTTTTTCATGTCCTTTATCAAGTTTGGATCATGTCATTTGCTATTTTCTTTCTGATGT
+ AAACTCTCAAAGTCTGAAGTGTATTGTCTTTTCCTGACACATATGTTGTAAATAATTTTC
+ TGGCTTACATTTTGACTTTTAATTTCATTCACGATGTTTTTAATGAATAATTTTAATTTT
+ TATGAATGCAAGTTAAAATAATTCTTTCATTGTGGTCTCTGACATGTCATGCCAATAAGG
+ GTCTTCTCCTCCAAGAGCACAGAAATATTTGCCAATACTGTCCTTAAAATCGGTCACAGT
+ TTCATTTTTTATATATGCATTTTACTTCAATTGGGGCTTCATTTTACTGAATGCCCTATT
+ TGAAGCAAGTTTCTCAGTTAATTCTTTTCTCAAAGGGCTAAGTATGGTAGATTGCAAACA
+ TAAGTGGCCACATAATGCTCTCACCTCctttgcctcctctcccaggaggagatagcgtcc
+ atctttccactccttaatctgggcttggccgtgtgacttgcactggccaatgggatatta
+ acaagtctgatgtgcacagaggctgtagaatgtgcacgggggcttggtctctcttgctgc
+ cctggagaccagctgccCCACGAAGGAACCAGAGCCAACCTGCTGCTTCCTGGAGGAAGA
+ CAGTCCCTCTGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGGAGAC
+ AGTCCCTCAGTCCCTCTGTCTCTGCCAACCAGTTAACCTGCTGCTTCCTGGAGGAAGACA
+ GTCACTCTGTCTCTGccaacccagttgaccgcagacatgcaggtctgctcaggtaagacc
+ agcacagtccctgccctgtgagccaaaccaaatggtccagccacagaatcgtgagcaaat
+ aagtgatgcttaagtcactaagatttgggCAAAAGCTGAGCATTTATCCCAATCCCAATA
+ CTGTTTGTCCTTCTGTTTATCTGTCTGTCCTTCCCTGCTCATTTAAAATGCCCCCACTGC
+ ATCTAGTACATTTTTATAGGATCAGGGATCTGCTCTTGGATTAATGTTGTGTTCCCACCT
+ CGAGGCAGCTTTGTAAGCTTCTGAGCACTTCCCAATTCCGGGTGACTTCAGGCACTGGGA
+ GGCCTGTGCATCAGCTGCTGCTGTCTGTAGCTGACTTCCTTCACCCCTCTGCTGTCCTCA
+ GCTCCTTCACCCCTGGGCCTCAGGAAATCAATGTCATGCTGACATCACTCTAGATCTAAA
+ AGTTGGGTTCTTGgaccaggcgtggtggctcacacctgtaatcccagcactttgggaggc
+ cgaggcgggtggatcacaaggtcaggagatcaagacgattctggctaacacggtgaaacc
+ ccgtctctactaaaaatacaaaaaaattagccgggtgtggtggcaggtgcctgtagcccc
+ agctacttgggaggctgaggcaggagaatggcttgaacctgggaggtggagcttgcagtg
+ agccaagatcacgccactgcactccagaatgggagagagagcgagactttctcaaaaaaa
+ aaaaaaaaaCTTAGGTTCTTGGATGTTCGGGAAAGGGGGTTATTATCTAGGATCCTTGAA
+ GCACCCCCAAGGGCATCTTCTCAAAGTTGGATGTGTGCATTTTCCTGAGAGGAAAGCTTT
+ CCCACATTATACAGCTTCTGAAAGGGTTGCTTGACCCACAGATGTGAAGCTGAGGCTGAA
+ GGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCAGCACCAGGTGGCAGCAGAGGTCA
+ GCAAGGCAAACCCGAGCCCGGGGATGCGGAGTGGGGGCAGCTACGTCCTCTCTTGAGCTA
+ CAGCAGATTCACTCTGTTCTGTTTCATTGTTGTTTAGTTTGCGTTGTGTTTCTCCAACTT
+ TGTGCCTCATCAGGAAAAGCTTTGGATCACAATTCCCAGtgctgaagaaaaggccaaact
+ cttggttgtgttctttgattAGTgcctgtgacgcagcttcaggaggtcctgagaacgtgt
+ gcacagtttagtcggcagaaacttagggaaatgtaagaccaccatcagcacataggagtt
+ ctgcattggtttggtctgcattggtttggtCTTTTCCTGGATACAGGTCTTGATAGGTCT
+ CTTGATGTCATTTCACTTCAGATTCTTCTTTAGAAAACTTGGACAATAGCATTTGCTGTC
+ TTGTCCAAATTGTTACTTCAAGTTTGCTCTTAGCAAGTAATTGTTTCAGTATCTATATCA
+ AAAATGGCTTAAGCCTGCAACATGTTTCTGAATGATTAACAAGGTGATAGTCAGTTCTTC
+ ATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCAG
+ >ENST00000426316.1
+ AATGATCAAATTATGTTTCCCATGCATCAGGTGCAATGGGAAGCTCTTctggagagtgag
+ agaagcttccagttaaggtgacattgaagccaagtcctgaaagatgaggaagagttgtat
+ gagagtggggagggaagggggaggtggagggaTGGGGAATGGGCCGGGATGGGATAGCGC
+ AAACTGCCCGGGAAGGGAAACCAGCACTGTACAGACCTGAACAACGAAGATGGCATATTT
+ TGTTCAGGGAATGGTGAATTAAGTGTGGCAGGAATGCTTTGTAGACACAGTAATTTGCTT
+ GTATGGAATTTTGCCTGAGAGACCTCATTCCTCACGTCGGCCATTCCAGGCCCCGTTTTT
+ CCCTTCCGGCAGCCTCTTGGCCTCTAATTTGTTTATCTTTTGTGTATAAATCCCAAAATA
+ TTGAATTTTGGAATATTTCCACCATTATGTAAATATTTTGATAGGTAA
diff --git a/docs/content/tools/groupby.rst b/docs/content/tools/groupby.rst
new file mode 100755
index 0000000..f28cc92
--- /dev/null
+++ b/docs/content/tools/groupby.rst
@@ -0,0 +1,237 @@
+.. _groupby:
+
+###############
+*groupby*
+###############
+``bedtools groupby`` is a useful tool that mimics the "group by" clause in database
+systems. Given a file or stream that is sorted by the appropriate "grouping
+columns" (``-g``), ``groupby`` will compute summary statistics on another
+column (``-c``) in the file or stream. This will work with output from all
+BEDTools as well as any other tab-delimited file or stream. As such, this is a
+generally useful tool for all command-line analyses, not just genomics related
+research.
+
+.. note::
+ When using ``bedtools groupby``, the input data must be ordered by the same
+ columns as specified with the ``-grp`` argument, which establish which
+ columns should be used to define a group of similar data. For example,
+ if ``-grp`` is 1,2,3, the data should be pre-grouped accordingly. When
+ ``bedtools groupby`` detects changes in the group columns it then summarizes
+ all lines with that group. For example, ``sort -k1,1 -k2,2 -k3,3 data.txt
+ | bedtools groupby -g 1,2,3 -c 4 -o mean``.
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+Usage
+::
+
+ bedtools groupby [OPTIONS] -i <input> -g <group columns> -c <op. column> -o <operation>
+
+or:
+::
+
+ groupBy [OPTIONS] -i <input> -g <group columns> -c <op. column> -o <operation>
+
+=========================== ===============================================================================================================================================================================================================
+Option Description
+=========================== ===============================================================================================================================================================================================================
+**-i** The input file that should be grouped and summarized. *Use "stdin" when using piped input*.
+ **Note: if -i is omitted, input is assumed to come from standard input (stdin)**
+**-g (-grp)** Specifies which column(s) (1-based) should be used to group the input. Columns may be comma-separated with each column must be explicitly listed. Or, ranges (e.g. 1-4) are also allowed. *Default: 1,2,3*
+**-c (-opCol)** Specify the column (1-based) that should be summarized. *Required*.
+**-o (-op)** Specify the operation that should be applied to **opCol**.
+
+ | Valid operations:
+
+ | **sum** - *numeric only*
+ | **count** - *numeric or text*
+ | **count_distinct** - *numeric or text*
+ | **min** - *numeric only*
+ | **max** - *numeric only*
+ | **mean** - *numeric only*
+ | **median** - *numeric only*
+ | **mode** - *numeric or text*
+ | **antimode** - *numeric or text*
+ | **stdev** - *numeric only*
+ | **sstdev** - *numeric only*
+ | **collapse** (i.e., print a comma separated list) - *numeric or text*
+ | **distinct** (i.e., print a comma separated list) - *numeric or text*
+ | **concat** (i.e., print a comma separated list) - *numeric or text*
+ | **freqasc** - *print a comma separated list of values observed and the number of times they were observed.*
+ | Reported in ascending order of frequency*
+ | **freqdesc** - *print a comma separated list of values observed and the number of times they were observed.*
+ | Reported in descending order of frequency*
+ | **first** - *numeric or text*
+ | **last** - *numeric or text*
+ | *Default: sum*
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+
+==========================================================================
+Default behavior.
+==========================================================================
+Let's imagine we have three incredibly interesting genetic variants that we are
+studying and we are interested in what annotated repeats these variants overlap.
+
+.. code-block:: bash
+
+ $ cat variants.bed
+ chr21 9719758 9729320 variant1
+ chr21 9729310 9757478 variant2
+ chr21 9795588 9796685 variant3
+
+ $ bedtools intersect -a variants.bed -b repeats.bed -wa -wb > variantsToRepeats.bed
+ $ cat variantsToRepeats.bed
+ chr21 9719758 9729320 variant1 chr21 9719768 9721892 ALR/Alpha 1004 +
+ chr21 9719758 9729320 variant1 chr21 9721905 9725582 ALR/Alpha 1010 +
+ chr21 9719758 9729320 variant1 chr21 9725582 9725977 L1PA3 3288 +
+ chr21 9719758 9729320 variant1 chr21 9726021 9729309 ALR/Alpha 1051 +
+ chr21 9729310 9757478 variant2 chr21 9729320 9729809 L1PA3 3897 -
+ chr21 9729310 9757478 variant2 chr21 9729809 9730866 L1P1 8367 +
+ chr21 9729310 9757478 variant2 chr21 9730866 9734026 ALR/Alpha 1036 -
+ chr21 9729310 9757478 variant2 chr21 9734037 9757471 ALR/Alpha 1182 -
+ chr21 9795588 9796685 variant3 chr21 9795589 9795713 (GAATG)n 308 +
+ chr21 9795588 9796685 variant3 chr21 9795736 9795894 (GAATG)n 683 +
+ chr21 9795588 9796685 variant3 chr21 9795911 9796007 (GAATG)n 345 +
+ chr21 9795588 9796685 variant3 chr21 9796028 9796187 (GAATG)n 756 +
+ chr21 9795588 9796685 variant3 chr21 9796202 9796615 (GAATG)n 891 +
+ chr21 9795588 9796685 variant3 chr21 9796637 9796824 (GAATG)n 621 +
+
+
+We can see that variant1 overlaps with 3 repeats, variant2 with 4 and variant3
+with 6. We can use bedtools groupby to summarize the hits for each variant in
+several useful ways. The default behavior is to compute the *sum* of the opCol.
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1,2,3 -c 9
+ chr21 9719758 9729320 6353
+ chr21 9729310 9757478 14482
+ chr21 9795588 9796685 3604
+
+
+
+==========================================================================
+Computing the min and max.
+==========================================================================
+Now let's find the *min* and *max* repeat score for each variant. We do this
+by "grouping" on the variant coordinate columns (i.e. cols. 1,2 and 3) and
+ask for the min and max of the repeat score column (i.e. col. 9).
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1,2,3 -c 9 -o min
+ chr21 9719758 9729320 1004
+ chr21 9729310 9757478 1036
+ chr21 9795588 9796685 308
+
+We can also group on just the *name* column with similar effect.
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 4 -c 9 -o min
+ variant1 1004
+ variant2 1036
+ variant3 308
+
+What about the *max* score? Let's keep the coordinates and the name of the
+variants so that we stay in BED format.
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -grp 1-4 -c 9 -o max
+ chr21 9719758 9729320 variant1 3288
+ chr21 9729310 9757478 variant2 8367
+ chr21 9795588 9796685 variant3 891
+
+
+
+==========================================================================
+Computing the mean and median.
+==========================================================================
+Now let's find the *mean* and *median* repeat score for each variant.
+
+.. code-block:: bash
+
+ $ cat variantsToRepeats.bed | bedtools groupby -g 1-4 -c 9 -o mean
+ chr21 9719758 9729320 variant1 1588.25
+ chr21 9729310 9757478 variant2 3620.5
+ chr21 9795588 9796685 variant3 600.6667
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1-4 -c 9 -op median
+ chr21 9719758 9729320 variant1 1030.5
+ chr21 9729310 9757478 variant2 2539.5
+ chr21 9795588 9796685 variant3 652
+
+
+==========================================================================
+Computing the mode and "antimode".
+==========================================================================
+Now let's find the *mode* and *antimode* (i.e., the least frequent) repeat
+score for each variant (in this case they are identical).
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1-4 -c 9 -o mode
+ chr21 9719758 9729320 variant1 1004
+ chr21 9729310 9757478 variant2 1036
+ chr21 9795588 9796685 variant3 308
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1-4 -c 9 -o antimode
+ chr21 9719758 9729320 variant1 1004
+ chr21 9729310 9757478 variant2 1036
+ chr21 9795588 9796685 variant3 308
+
+
+
+==========================================================================
+Computing the count of lines for a given group.
+==========================================================================
+Figure:
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -g 1-4 -c 9 -c count
+ chr21 9719758 9729320 variant1 4
+ chr21 9729310 9757478 variant2 4
+ chr21 9795588 9796685 variant3 6
+
+
+
+
+============================================================================
+Collapsing: listing all of the values in the opCol for a given group.
+============================================================================
+Now for something different. What if we wanted all of the names of the repeats
+listed on the same line as the variants? Use the collapse option. This
+"denormalizes" things. Now you have a list of all the repeats on a single line.
+
+.. code-block:: bash
+
+ $ bedtools groupby -i variantsToRepeats.bed -grp 1-4 -c 9 -o collapse
+ chr21 9719758 9729320 variant1 ALR/Alpha,ALR/Alpha,L1PA3,ALR/Alpha,
+ chr21 9729310 9757478 variant2 L1PA3,L1P1,ALR/Alpha,ALR/Alpha,
+ chr21 9795588 9796685 variant3 (GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,(GAATG)n,
+
+
+
+==========================================================================
+Computing frequencies: freqasc and freqdesc.
+==========================================================================
+What if we want to report each distinct value along with its number of
+occurrence (much like uniq -c)? The ``freqasc`` and freqdesc`` operations
+handle this.
+
+.. code-block:: bash
+
+ $ cat variantsToRepeats.bed | bedtools groupby -g 1 -c 8 -o freqdesc
+ chr21 (GAATG)n:6,ALR/Alpha:5,L1PA3:2,L1P1:1,
+
+ $ cat variantsToRepeats.bed | bedtools groupby -g 1 -c 8 -o freqasc
+ chr21 L1P1:1,L1PA3:2,ALR/Alpha:5,(GAATG)n:6,
+
diff --git a/docs/content/tools/igv.rst b/docs/content/tools/igv.rst
new file mode 100644
index 0000000..2f1eb00
--- /dev/null
+++ b/docs/content/tools/igv.rst
@@ -0,0 +1,5 @@
+.. _igv:
+
+###############
+*igv*
+###############
diff --git a/docs/content/tools/intersect.rst b/docs/content/tools/intersect.rst
new file mode 100755
index 0000000..735f391
--- /dev/null
+++ b/docs/content/tools/intersect.rst
@@ -0,0 +1,670 @@
+.. _intersect:
+
+#########################################
+*intersect*
+#########################################
+
+|
+
+.. image:: ../images/tool-glyphs/intersect-glyph.png
+ :width: 600pt
+
+|
+
+By far, the most common question asked of two sets of genomic features
+is whether or not any of the features in the two sets "overlap"
+with one another. This is known as feature intersection.
+``bedtools intersect`` allows one to screen for overlaps between
+two sets of genomic features. Moreover, it allows one to have fine control
+as to how the intersections are reported. ``bedtools intersect`` works
+with both BED/GFF/VCF and BAM files as input.
+
+.. note::
+
+ If you are trying to intersect very large files and are having trouble
+ with excessive memory usage, please presort your data by chromosome and
+ then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
+ for BED files) and then use the ``-sorted`` option. This invokes a
+ memory-efficient algorithm designed for large files.
+
+.. seealso::
+
+ :doc:`../tools/subtract`
+ :doc:`../tools/window`
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools intersect [OPTIONS] -a <BED/BAM/GFF/VCF> -b <BED/BAM/GFF/VCF>
+
+**(or)**:
+::
+
+ intersectBed [OPTIONS] -a <BED/BAM/GFF/VCF> -b <BED/GFF/VCF>
+
+
+
+
+=========================== =========================================================================================================================================================
+Option Description
+=========================== =========================================================================================================================================================
+**-a** BED/GFF/VCF file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
+**-b** BED/GFF/VCF file B. Use "stdin" if passing B with a UNIX pipe.
+**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools intersect -abam stdin -b genes.bed
+**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
+**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: ``bedtools intersect -abam reads.bam -b genes.bed -bed``
+**-wa** Write the original entry in A for each overlap.
+**-wb** Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by -f and -r.
+**-loj** Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B.
+**-wo** Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by -f and -r.
+**-wao** Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by -f and -r.
+**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. Restricted by -f and -r.
+**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B. Restricted by -f and -r.
+**-v** Only report those entries in A that have no overlap in B. Restricted by -f and -r.
+**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
+**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
+**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
+**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
+**-split** Treat "split" BAM (i.e., having an "N" CIGAR operation) or BED12 entries as distinct BED intervals.
+**-sorted** For very large B files, invoke a "sweeping" algorithm that requires position-sorted (e.g., ``sort -k1,1 -k2,2n`` for BED files) input.
+ When using -sorted, memory usage remains low even for very large files.
+**-g** Specify a genome file the defines the expected chromosome order in the input files for use with the ``-sorted`` option.
+**-header** Print the header from the A file prior to results.
+=========================== =========================================================================================================================================================
+
+
+===============================
+Default behavior
+===============================
+By default, if an overlap is found, ``bedtools intersect`` reports the shared interval between the two
+overlapping features.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed
+ chr1 15 20
+
+
+
+=============================================
+``-wa`` Reporting the original A feature
+=============================================
+Instead, one can force ``bedtools intersect`` to report the *original* **"A"** feature when an overlap is found. As
+shown below, the entire "A" feature is reported, not just the portion that overlaps with the "B" feature.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed -wa
+ chr1 10 20
+
+
+=============================================
+``-wb`` Reporting the original B feature
+=============================================
+Similarly, one can force ``bedtools intersect`` to report the *original* **"B"** feature when an overlap is found. If
+just -wb is used, the overlapping portion of A will be reported followed by the *original* **"B"**. If both -wa
+and -wb are used, the *originals* of both **"A"** and **"B"** will be reported.
+
+For example (-wb alone):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed -wb
+ chr1 15 20 chr 15 20
+
+
+Now -wa and -wb:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed -wa -wb
+ chr1 10 20 chr 15 20
+
+========================================================================
+``-loj`` Left outer join. Report features in A with and without overlaps
+========================================================================
+By default, ``bedtools intersect`` will only report features in A that
+have an overlap in B. The ``-loj`` option will report every A feature
+no matter what. When there is an overlap (or more than 1), it will report
+A with its overlaps. Yet when there are no overlaps, an A feature will be
+reported with a NULL B feature to indicate that there were no overlaps
+
+For example (*without* ``-loj``):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed
+ chr1 10 20 chr 15 20
+
+Now *with* ``-loj``:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed -loj
+ chr1 10 20 chr 15 20
+ chr1 30 40 . -1 -1
+
+
+=======================================================================
+``-wo`` Write the *amount* of overlap between intersecting features
+=======================================================================
+The ``-wo`` option reports a column after each combination of intersecting
+"A" and "B" features indicating the *amount* of overlap in bases pairs that
+is observed between the two features.
+
+.. note::
+
+ When an interval in A does not intersect an interval in B, it will not be
+ reported. If you would like to report such intervals with an overlap equal
+ to 0, see the ``-wao`` option.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+ chr1 18 25
+
+ $ bedtools intersect -a A.bed -b B.bed -wo
+ chr1 10 20 chr1 15 20 5
+ chr1 10 20 chr1 18 25 2
+
+
+=======================================================================
+``-wao`` Write *amounts* of overlap for all features.
+=======================================================================
+The ``-wao`` option extends upon the ``-wo`` option in that, unlike ``-wo``,
+it reports an overlap of 0 for features in A that do not have an intersection
+in B.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+ chr1 18 25
+
+ $ bedtools intersect -a A.bed -b B.bed -wao
+ chr1 10 20 chr1 15 20 5
+ chr1 10 20 chr1 18 25 2
+ chr1 30 40 . -1 -1 0
+
+==========================================================================
+``-u`` (unique) Reporting the mere presence of *any* overlapping features
+==========================================================================
+Often you'd like to simply know a feature in "A" overlaps one or more
+features in B without reporting each and every intersection. The ``-u``
+option will do exactly this: if an one or more overlaps exists, the
+A feature is reported. Otherwise, nothing is reported.
+
+For example, without ``-u``:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+
+ $ cat B.bed
+ chr1 15 20
+ chr1 17 22
+
+ $ bedtools intersect -a A.bed -b B.bed
+ chr1 10 20
+ chr1 10 20
+
+Now with ``-u``:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+
+ $ cat B.bed
+ chr1 15 20
+ chr1 17 22
+
+ $ bedtools intersect -a A.bed -b B.bed -u
+ chr1 10 20
+
+
+=======================================================================
+``-c`` Reporting the number of overlapping features
+=======================================================================
+The -c option reports a column after each "A" feature indicating the *number* (0 or more) of overlapping
+features found in "B". Therefore, *each feature in A is reported once*.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+ chr1 18 25
+
+ $ bedtools intersect -a A.bed -b B.bed -c
+ chr1 10 20 2
+ chr1 30 40 0
+
+
+
+
+=======================================================================
+``-v`` Reporting the absence of any overlapping features
+=======================================================================
+There will likely be cases where you'd like to know which "A" features
+do not overlap with any of the "B" features. Perhaps you'd like to know
+which SNPs don't overlap with any gene annotations. The ``-v``
+(an homage to "grep -v") option will only report those "A" features
+that have no overlaps in "B".
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat B.bed
+ chr1 15 20
+
+ $ bedtools intersect -a A.bed -b B.bed -v
+ chr1 30 40
+
+
+
+=======================================================================
+``-f`` Requiring a minimal overlap fraction
+=======================================================================
+By default, ``bedtools intersect`` will report an overlap between A and B so long as there is at least one base
+pair is overlapping. Yet sometimes you may want to restrict reported overlaps between A and B to cases
+where the feature in B overlaps at least X% (e.g. 50%) of the A feature. The -f option does exactly
+this.
+
+For example (note that the second B entry is not reported):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 130 201
+ chr1 180 220
+
+ $ bedtools intersect -a A.bed -b B.bed -f 0.50 -wa -wb
+ chr1 100 200 chr1 130 201
+
+==========================================================================
+``-r, and -f`` Requiring reciprocal minimal overlap fraction
+==========================================================================
+Similarly, you may want to require that a minimal fraction of both the A and the B features is
+overlapped. For example, if feature A is 1kb and feature B is 1Mb, you might not want to report the
+overlap as feature A can overlap at most 1% of feature B. If one set -f to say, 0.02, and one also
+enable the -r (reciprocal overlap fraction required), this overlap would not be reported.
+
+For example (note that the second B entry is not reported):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 130 201
+ chr1 130 200000
+
+ $ bedtools intersect -a A.bed -b B.bed -f 0.50 -r -wa -wb
+ chr1 100 200 chr1 130 201
+
+==========================================================================
+``-s`` Enforcing *same* strandedness
+==========================================================================
+By default, ``bedtools intersect`` will report overlaps between features
+even if the features are on opposite strands. However, if strand information
+is present in both BED files and the "-s" option is used, overlaps will only
+be reported when features are on the same strand.
+
+For example (note that the first B entry is not reported):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 100 +
+
+ $ cat B.bed
+ chr1 130 201 b1 100 -
+ chr1 132 203 b2 100 +
+
+ $ bedtools intersect -a A.bed -b B.bed -wa -wb -s
+ chr1 100 200 a1 100 + chr1 132 203 b2 100 +
+
+
+==========================================================================
+``-S`` Enforcing *opposite* "strandedness"
+==========================================================================
+The ``-s`` option enforces that overlaps be on the *same* strand. In some
+cases, you may want to enforce that overlaps be found on *opposite* strands.
+In this, case use the ``-S`` option.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 100 +
+
+ $ cat B.bed
+ chr1 130 201 b1 100 -
+ chr1 132 203 b2 100 +
+
+ $ bedtools intersect -a A.bed -b B.bed -wa -wb -S
+ chr1 100 200 a1 100 + chr1 130 201 b1 100 -
+
+
+==========================================================================
+``-abam`` Default behavior when using BAM input (deprecated since 2.18.0)
+==========================================================================
+When comparing alignments in BAM format (**-abam**) to features in BED format (**-b**), ``bedtools intersect``
+will, **by default**, write the output in BAM format. That is, each alignment in the BAM file that meets
+the user's criteria will be written (to standard output) in BAM format. This serves as a mechanism to
+create subsets of BAM alignments are of biological interest, etc. Note that only the mate in the BAM
+alignment is compared to the BED file. Thus, if only one end of a paired-end sequence overlaps with a
+feature in B, then that end will be written to the BAM output. By contrast, the other mate for the
+pair will not be written. One should use **pairToBed(Section 5.2)** if one wants each BAM alignment
+for a pair to be written to BAM output.
+
+.. code-block:: bash
+
+ $ bedtools intersect -abam reads.unsorted.bam -b simreps.bed | \
+ samtools view - | \
+ head -3
+
+ BERTHA_0001:3:1:15:1362#0 99 chr4 9236904 0 50M = 9242033 5 1 7 9
+ AGACGTTAACTTTACACACCTCTGCCAAGGTCCTCATCCTTGTATTGAAG W c T U ] b \ g c e g X g f c b f c c b d d g g V Y P W W _
+ \c`dcdabdfW^a^gggfgd XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:19 X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:50
+ BERTHA _0001:3:1:16:994#0 83 chr6 114221672 37 25S6M1I11M7S =
+ 114216196 -5493 G A A A G G C C A G A G T A T A G A A T A A A C A C A A C A A T G T C C A A G G T A C A C T G T T A
+ gffeaaddddggggggedgcgeggdegggggffcgggggggegdfggfgf XT:A:M NM:i:3 SM:i:37 AM:i:37 XM:i:2 X O : i :
+ 1 XG:i:1 MD:Z:6A6T3
+ BERTHA _0001:3:1:16:594#0 147 chr8 43835330 0 50M =
+ 43830893 -4487 CTTTGGGAGGGCTTTGTAGCCTATCTGGAAAAAGGAAATATCTTCCCATG U
+ \e^bgeTdg_Kgcg`ggeggg_gggggggggddgdggVg\gWdfgfgff XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:10 X1:i:7 X M : i :
+ 2 XO:i:0 XG:i:0 MD:Z:1A2T45
+
+.. note::
+
+ As of version 2.18.0, it is no longer necessary to specify a BAM input file via ``-abam``.
+ Bedtools now autodetects this when ``-a`` is used.
+
+
+
+==========================================================================
+``-ubam`` Default behavior when using BAM input
+==========================================================================
+The ``-ubam`` option writes *uncompressed* BAM output to stdout. This is
+useful for increasing the speed of pipelines that accept the output of
+``bedtools`` intersect as input, since the receiving tool does not need to
+uncompress the data.
+
+==========================================================================
+``-bed`` Output BED format when using BAM input
+==========================================================================
+When comparing alignments in BAM format (**-abam**) to features in BED format (**-b**), ``bedtools intersect``
+will **optionally** write the output in BED format. That is, each alignment in the BAM file is converted
+to a 6 column BED feature and if overlaps are found (or not) based on the user's criteria, the BAM
+alignment will be reported in BED format. The BED "name" field is comprised of the RNAME field in
+the BAM alignment. If mate information is available, the mate (e.g., "/1" or "/2") field will be
+appended to the name. The "score" field is the mapping quality score from the BAM alignment.
+
+.. code-block:: bash
+
+ $ bedtools intersect -abam reads.unsorted.bam -b simreps.bed -bed | head -20
+
+ chr4 9236903 9236953 BERTHA_0001:3:1:15:1362#0/1 0 +
+ chr6 114221671 114221721 BERTHA_0001:3:1:16:994#0/1 37 -
+ chr8 43835329 43835379 BERTHA_0001:3:1:16:594#0/2 0 -
+ chr4 49110668 49110718 BERTHA_0001:3:1:31:487#0/1 23 +
+ chr19 27732052 27732102 BERTHA_0001:3:1:32:890#0/2 46 +
+ chr19 27732012 27732062 BERTHA_0001:3:1:45:1135#0/1 37 +
+ chr10 117494252 117494302 BERTHA_0001:3:1:68:627#0/1 37 -
+ chr19 27731966 27732016 BERTHA_0001:3:1:83:931#0/2 9 +
+ chr8 48660075 48660125 BERTHA_0001:3:1:86:608#0/2 37 -
+ chr9 34986400 34986450 BERTHA_0001:3:1:113:183#0/2 37 -
+ chr10 42372771 42372821 BERTHA_0001:3:1:128:1932#0/1 3 -
+ chr19 27731954 27732004 BERTHA_0001:3:1:130:1402#0/2 0 +
+ chr10 42357337 42357387 BERTHA_0001:3:1:137:868#0/2 9 +
+ chr1 159720631 159720681 BERTHA_0001:3:1:147:380#0/2 37 -
+ chrX 58230155 58230205 BERTHA_0001:3:1:151:656#0/2 37 -
+ chr5 142612746 142612796 BERTHA_0001:3:1:152:1893#0/1 37 -
+ chr9 71795659 71795709 BERTHA_0001:3:1:177:387#0/1 37 +
+ chr1 106240854 106240904 BERTHA_0001:3:1:194:928#0/1 37 -
+ chr4 74128456 74128506 BERTHA_0001:3:1:221:724#0/1 37 -
+ chr8 42606164 42606214 BERTHA_0001:3:1:244:962#0/1 37 +
+
+==================================================================================
+``-split`` Reporting overlaps with spliced alignments or blocked BED features
+==================================================================================
+As described in section 1.3.19, bedtools intersect will, by default, screen for overlaps against the entire span
+of a spliced/split BAM alignment or blocked BED12 feature. When dealing with RNA-seq reads, for
+example, one typically wants to only screen for overlaps for the portions of the reads that come from
+exons (and ignore the interstitial intron sequence). The **-split** command allows for such overlaps to be
+performed.
+
+For example, the diagram below illustrates the *default* behavior. The blue dots represent the "split/
+spliced" portion of the alignment (i.e., CIGAR "N" operation). In this case, the two exon annotations
+are reported as overlapping with the "split" BAM alignment, but in addition, a third feature that
+overlaps the "split" portion of the alignment is also reported.
+
+::
+ Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ Exons --------------- ----------
+
+ BED/BAM A ************.......................................****
+
+ BED File B ^^^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^
+
+ Result =============== ======== ==========
+
+
+In contrast, when using the **-split** option, only the exon overlaps are reported.
+
+::
+ Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ Exons --------------- ----------
+
+ BED/BAM A ************.......................................****
+
+ BED File B ^^^^^^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^
+
+ Result =============== ==========
+
+
+==========================================================================
+``-sorted`` Invoke a memory-efficient algorithm for very large files.
+==========================================================================
+The default algorithm for detecting overlaps loads the B file into an R-tree
+structure in memory. While fast, it can consume substantial memory for large
+files. For these reason, we provide an alternative, memory efficient algorithm
+that depends upon inout files that have been sorted by chromosome and then by
+start position. When both input files are position-sorted, the algorithm can
+"sweep" through the data and detect overlaps on the fly in a manner much
+like the way database systems join two tables. This option is invoked with the
+``-sorted`` option.
+
+.. note::
+
+ By default, the ``-sorted`` option requires that the records are **GROUPED**
+ by chromosome and that within each chromosome group, the records are sorted by
+ chromosome position. One way to achieve this (for BED files for example) is use
+ the UNIX sort utility to sort both files by chromosome and then by position.
+ That is, ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``. However, since we merely
+ require that the chromsomes are grouped (that is, all records for a given chromosome
+ come in a single block in the file), sorting criteria other than the alphanumeric
+ criteria that is used by the ``sort`` utility are fine. For example, you could use
+ the "version sort" (``-V``) option in newer versions of GNU sort to make the chromosomes
+ come in this (chr1, chr2, chr3) order instead of this (chr1, chr10, chr11) order.
+
+
+For example:
+
+.. code-block:: bash
+
+ $ bedtools intersect -a big.sorted.bed -b huge.sorted.bed -sorted
+
+
+==========================================================================
+``-g`` Define an alternate chromosome sort order via a genome file.
+==========================================================================
+As described above, the ``-sorted`` option expects that the input files are grouped
+by chromosome. However, there arise cases where ones input
+files are sorted by a different criteria and it is to computationally onerous
+to resort the files alphanumerically. For example, the GATK expects that
+BAM files are sorted in a very specific manner. The ``-g`` option allows
+one to specify an exact ording that should be expected in the input (e.g.,
+BAM, BED, etc.) files. All you need to do is re-order you genome file to
+specify the order. Also, the use of a genome file to specify the expected
+order allows the ``intersect`` tool to detect when two files are internally
+grouped but each file actually follows a different order. This will cause
+incorrect results and the ``-g`` file will alert you to such problems.
+
+For example, an alphanumerically ordered genome file would look like the
+following:
+
+.. code-block:: bash
+
+ $ cat hg19.genome
+ chr1 249250621
+ chr10 135534747
+ chr11 135006516
+ chr12 133851895
+ chr13 115169878
+ chr14 107349540
+ chr15 102531392
+ chr16 90354753
+ chr17 81195210
+ chr18 78077248
+ chr19 59128983
+ chr2 243199373
+ chr20 63025520
+ chr21 48129895
+ chr22 51304566
+ chr3 198022430
+ chr4 191154276
+ chr5 180915260
+ chr6 171115067
+ chr7 159138663
+ chr8 146364022
+ chr9 141213431
+ chrM 16571
+ chrX 155270560
+ chrY 59373566
+
+However, if your input BAM or BED files are ordered such as ``chr1, chr2, chr3``, etc.,
+one need to simply reorder the genome file accordingly:
+
+.. code-block:: bash
+
+ $ sort -k1,1V hg19.genome > hg19.versionsorted.genome
+ $ cat hg19.versionsorted.genome
+ chr1 249250621
+ chr2 243199373
+ chr3 198022430
+ chr4 191154276
+ chr5 180915260
+ chr6 171115067
+ chr7 159138663
+ chr8 146364022
+ chr9 141213431
+ chr10 135534747
+ chr11 135006516
+ chr12 133851895
+ chr13 115169878
+ chr14 107349540
+ chr15 102531392
+ chr16 90354753
+ chr17 81195210
+ chr18 78077248
+ chr19 59128983
+ chr20 63025520
+ chr21 48129895
+ chr22 51304566
+ chrM 16571
+ chrX 155270560
+ chrY 59373566
+
+At this point, one can now use the ``-sorted`` option along with the genome file
+in order to properly process the input files that abide by something other than an
+alphanumeric sorting order.
+
+.. code-block:: bash
+
+ $ bedtools intersect -a a.versionsorted.bam -b b.versionsorted.bed \
+ -sorted \
+ -g hg19.versionsorted.genome
+
+Et voila.
+
+
+==========================================================================
+``-header`` Print the header for the A file before reporting results.
+==========================================================================
+By default, if your A file has a header, it is ignored when reporting results.
+This option will instead tell bedtools to first print the header for the
+A file prior to reporting results.
+
diff --git a/docs/content/tools/jaccard.rst b/docs/content/tools/jaccard.rst
new file mode 100644
index 0000000..268f945
--- /dev/null
+++ b/docs/content/tools/jaccard.rst
@@ -0,0 +1,110 @@
+.. _jaccard:
+
+###############
+*jaccard*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/jaccard-glyph.png
+ :width: 600pt
+
+Whereas the bedtools ``intersect`` tool enumerates each an every intersection between two sets of genomic
+intervals, one often needs a single statistic reflecting the *similarity* of the two sets based on the
+intersections between them. The Jaccard statistic is used in set theory to represent the ratio of the
+intersection of two sets to the union of the two sets. Similarly, Favorov et al [1] reported the use
+of the Jaccard statistic for genome intervals: specifically, it measures the ratio of the number of
+intersecting base pairs between two sets to the number of base pairs in the union of the two sets.
+The bedtools jaccard tool implements this statistic, yet modifies the statistic such that the length of the
+intersection is subtracted from the length of the union. As a result, the final statistic ranges from 0.0
+to 1.0, where 0.0 represents no overlap and 1.0 represent complete overlap.
+
+.. code::
+
+ [1] Exploring Massive, Genome Scale Datasets with the GenometriCorr Package.
+ Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, et al. (2012)
+ PLoS Comput Biol 8(5): e1002529. doi:10.1371/journal.pcbi.1002529
+
+
+.. note::
+
+ The ``jaccard`` tool requires that your data is pre-sorted by chromosome and
+ then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
+ for BED files).
+
+.. seealso::
+
+ :doc:`../tools/reldist`
+ :doc:`../tools/intersect`
+
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools jaccard [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+
+=========================== =========================================================================================================================================================
+Option Description
+=========================== =========================================================================================================================================================
+**-a** BED/GFF/VCF file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
+**-b** BED/GFF/VCF file B. Use "stdin" if passing B with a UNIX pipe.
+**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
+**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
+=========================== =========================================================================================================================================================
+
+
+===============================
+Default behavior
+===============================
+By default, ``bedtools jaccard`` reports the length of the intersection, the length of the union (minus the intersection),
+the final Jaccard statistic reflecting the similarity of the two sets, as well as the number of intersections.
+
+.. code-block:: bash
+
+ $ cat a.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat b.bed
+ chr1 15 20
+
+ $ bedtools jaccard -a a.bed -b b.bed
+ intersection union jaccard n_intersections
+ 5 20 0.25 1
+
+============================================
+Controlling which intersections are included
+============================================
+One can also control which intersections are included in the statistic by requiring a certain fraction of overlap
+with respect to the features in A (via the ``-f`` parameter) or also by requiring that the fraction of overlap is
+reciprocal (``-r``) in A and B.
+
+.. code-block:: bash
+
+ $ cat a.bed
+ chr1 10 20
+ chr1 30 40
+
+ $ cat b.bed
+ chr1 15 20
+
+Require 10% overlap with respect to the intervals in A:
+
+.. code-block:: bash
+
+ $ bedtools jaccard -a a.bed -b b.bed -f 0.1
+ intersection union jaccard n_intersections
+ 5 20 0.25 1
+
+Require 60% overlap with respect to the intervals in A:
+
+.. code-block:: bash
+
+ $ bedtools jaccard -a a.bed -b b.bed -f 0.6
+ intersection union jaccard n_intersections
+ 0 25 0.25 0
+
diff --git a/docs/content/linksBed.rst b/docs/content/tools/links.rst
similarity index 95%
rename from docs/content/linksBed.rst
rename to docs/content/tools/links.rst
index ca32e8b..cbdbee6 100755
--- a/docs/content/linksBed.rst
+++ b/docs/content/tools/links.rst
@@ -1,14 +1,17 @@
+.. _links:
+
###############
-5.16 linksBed
+*links*
###############
Creates an HTML file with links to an instance of the UCSC Genome Browser for all features /
intervals in a file. This is useful for cases when one wants to manually inspect through a large set of
annotations or features.
==========================================================================
-5.16.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
linksBed [OPTIONS] -i <BED/GFF/VCF> > <HTML file>
@@ -24,11 +27,12 @@ Usage:
==========================================================================
-5.16.2 Default behavior
+Default behavior
==========================================================================
By default, **linksBed** creates links to the public UCSC Genome Browser.
For example:
+
::
head genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
@@ -52,11 +56,12 @@ link on the page is built from the features in genes.bed:
==========================================================================
-5.16.3 Creating HTML links to a local UCSC Browser installation
+Creating HTML links to a local UCSC Browser installation
==========================================================================
Optionally, **linksBed** will create links to a local copy of the UCSC Genome Browser.
For example:
+
::
head -3 genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
@@ -65,6 +70,7 @@ For example:
linksBed -i genes.bed -base http://mirror.uni.edu > genes.html
One can point the links to the appropriate organism and genome build as well:
+
::
head -3 genes.bed
chr21 9928613 10012791 uc002yip.1 0 -
diff --git a/docs/content/tools/makewindows.rst b/docs/content/tools/makewindows.rst
new file mode 100644
index 0000000..b95f150
--- /dev/null
+++ b/docs/content/tools/makewindows.rst
@@ -0,0 +1,5 @@
+.. _makewindows:
+
+###############
+*makewindows*
+###############
diff --git a/docs/content/tools/map.rst b/docs/content/tools/map.rst
new file mode 100644
index 0000000..880aea1
--- /dev/null
+++ b/docs/content/tools/map.rst
@@ -0,0 +1,191 @@
+.. _map:
+
+###############
+*map*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/map-glyph.png
+ :width: 600pt
+ :align: center
+
+|
+
+``bedtools map`` allows one to map overlapping features in a B file onto
+features in an A file and apply statistics and/or summary operations on those
+features.
+
+For example, one could use ``bedtools map`` to compute the average
+score of BEDGRAPH records that overlap genes. Since the fourth column in
+BEDGRAPH is the score, the following command illustrates how this would be done:
+
+.. code-block:: bash
+
+ $ bedtools map -a genes.bed -b peaks.bedgraph -c 4 -o mean
+
+Another example is discussed in this Biostars
+`post <http://www.biostars.org/p/61653/>`_.
+
+
+.. note::
+
+ ``bedtools map`` requires each input file to be sorted by genome coordinate.
+ For BED files, this can be done with ``sort -k1,1 -k2,2n``.
+
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools map [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
+
+**(or)**:
+::
+
+ mapBed [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
+
+
+=========================== ===============================================================================================================================================================================================================
+Option Description
+=========================== ===============================================================================================================================================================================================================
+**-c** | Specify the column from the B file to map onto intervals in A.
+ | ``Default: 5``
+
+**-o** Specify the operation that should be applied to ``-c``.
+
+ | Valid operations:
+
+ | **sum** - *numeric only*
+ | **count** - *numeric or text*
+ | **count_distinct** - *numeric or text*
+ | **min** - *numeric only*
+ | **max** - *numeric only*
+ | **absmin** - *numeric only*
+ | **absmax** - *numeric only*
+ | **mean** - *numeric only*
+ | **median** - *numeric only*
+ | **antimode** - *numeric or text*
+ | **collapse** (i.e., print a comma separated list) - *numeric or text*
+ | **distinct** (i.e., print a comma separated list) - *numeric or text*
+ | **concat** (i.e., print a comma separated list) - *numeric or text*
+ |
+ | ``Default: 5``
+
+**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
+**-r** Require that the fraction of overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.
+**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
+**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
+**-null** | The value to print if no overlaps are found for an A interval.
+ | ``Default: "."``
+
+**-header** Print the header from the A file prior to results.
+**-split** Treat "split" BAM (i.e., having an "N" CIGAR operation) or BED12 entries as distinct BED intervals.
+ When using -sorted, memory usage remains low even for very large files.
+**-g** Specify a genome file the defines the expected chromosome order in the input files.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+================================================================================
+Default behavior - compute the ``sum`` of the ``score`` column for all overlaps.
+================================================================================
+By default, ``map`` computes the sum of the 5th column (the ``score`` field for
+BED format) for all intervals in B that overlap each interval in A.
+
+.. tip::
+
+ Records in A that have no overlap will, by default, return ``.`` for the
+ computed value from B. This can be changed with the ``-null`` option.
+
+.. code-block:: bash
+
+ $ cat a.bed
+ chr1 10 20 a1 1 +
+ chr1 50 60 a2 2 -
+ chr1 80 90 a3 3 -
+
+ $ cat b.bed
+ chr1 12 14 b1 2 +
+ chr1 13 15 b2 5 -
+ chr1 16 18 b3 5 +
+ chr1 82 85 b4 2 -
+ chr1 85 87 b5 3 +
+
+ $ bedtools map -a a.bed -b b.bed
+ chr1 10 20 a1 1 + 12
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 5
+
+
+================================================================================
+``mean`` Compute the mean of a column from overlapping intervals
+================================================================================
+
+.. code-block:: bash
+
+ $ cat a.bed
+ chr1 10 20 a1 1 +
+ chr1 50 60 a2 2 -
+ chr1 80 90 a3 3 -
+
+ $ cat b.bed
+ chr1 12 14 b1 2 +
+ chr1 13 15 b2 5 -
+ chr1 16 18 b3 5 +
+ chr1 82 85 b4 2 -
+ chr1 85 87 b5 3 +
+
+ $ bedtools map -a a.bed -b b.bed -c 5 -o mean
+ chr1 10 20 a1 1 + 4
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 2.5
+
+
+================================================================================
+``collapse`` List each value of a column from overlapping intervals
+================================================================================
+
+.. code-block:: bash
+
+ $ bedtools map -a a.bed -b b.bed -c 5 -o collapse
+ chr1 10 20 a1 1 + 2,5,5
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 2,3
+
+
+================================================================================
+``distinct`` List each *unique* value of a column from overlapping intervals
+================================================================================
+
+.. code-block:: bash
+
+ $ bedtools map -a a.bed -b b.bed -c 5 -o distinct
+ chr1 10 20 a1 1 + 2,5
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 2,3
+
+================================================================================
+``-s`` Only include intervals that overlap on the *same* strand.
+================================================================================
+
+.. code-block:: bash
+
+ $ bedtools map -a a.bed -b b.bed -c 5 -o collapse -s
+ chr1 10 20 a1 1 + 2,5
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 2
+
+================================================================================
+``-S`` Only include intervals that overlap on the *opposite* strand.
+================================================================================
+
+.. code-block:: bash
+
+ $ bedtools map -a a.bed -b b.bed -c 5 -o collapse -S
+ chr1 10 20 a1 1 + 5
+ chr1 50 60 a2 2 - .
+ chr1 80 90 a3 3 - 3
diff --git a/docs/content/tools/maskfasta.rst b/docs/content/tools/maskfasta.rst
new file mode 100755
index 0000000..c453aca
--- /dev/null
+++ b/docs/content/tools/maskfasta.rst
@@ -0,0 +1,115 @@
+.. _maskfasta:
+
+###############
+*maskfasta*
+###############
+
+
+|
+
+.. image:: ../images/tool-glyphs/maskfasta-glyph.png
+ :width: 600pt
+
+
+``bedtools maskfasta`` masks sequences in a FASTA file based on intervals defined in a feature file. The
+headers in the input FASTA file must exactly match the chromosome column in the feature file. This
+may be useful fro creating your own masked genome file based on custom annotations or for masking all
+but your target regions when aligning sequence data from a targeted capture experiment.
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**
+
+.. code-block:: bash
+
+ $ bedtools maskfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
+
+**(or):**
+
+.. code-block:: bash
+
+ $ maskFastaFromBed [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
+
+
+.. note::
+
+ The input (``-fi``) and output (``-fo``) FASTA files must be different.
+
+.. seealso::
+
+ :doc:`../tools/getfasta`
+
+
+=========================== ==========================================================================================================================================
+ Option Description
+=========================== ==========================================================================================================================================
+**-soft** Soft-mask (that is, convert to lower-case bases) the FASTA sequence. *By default, hard-masking (that is, conversion to Ns) is performed*.
+**-mc** Replace masking character. That is, instead of masking with Ns, use another character.
+=========================== ==========================================================================================================================================
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+**bedtools maskfasta** will mask a FASTA file based on the intervals in a
+BED file. The newly masked FASTA file is written to the output FASTA file.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10
+
+ $ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out
+
+ $ cat test.fa.out
+ >chr1
+ AAAAANNNNNCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+
+==========================================================================
+``-soft`` Soft-masking the FASTA file.
+==========================================================================
+Using the **-soft** option, one can optionally "soft-mask" the FASTA file.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10
+
+ $ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -soft
+
+ $ cat test.fa.out
+ >chr1
+ AAAAAaaaccCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+==========================================================================
+``-mc`` Specify a masking character.
+==========================================================================
+Using the **-mc** option, one can optionally choose a masking character to each
+base that will be masked by the BED file.
+
+.. code-block:: bash
+
+ $ cat test.fa
+ >chr1
+ AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
+
+ $ cat test.bed
+ chr1 5 10
+
+ $ bedtools maskfasta -fi test.fa -bed test.bed -fo test.fa.out -mc X
+
+ $ cat test.fa.out
+ >chr1
+ AAAAAXXXXXCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
diff --git a/docs/content/tools/merge.rst b/docs/content/tools/merge.rst
new file mode 100755
index 0000000..e6b35e8
--- /dev/null
+++ b/docs/content/tools/merge.rst
@@ -0,0 +1,219 @@
+.. _merge:
+
+###############
+*merge*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/merge-glyph.png
+ :width: 600pt
+|
+
+
+
+``bedtools merge`` combines overlapping or "book-ended" features in an interval
+file into a single feature which spans all of the combined features.
+
+.. note::
+
+ ``bedtools merge`` requires that you presort your data by chromosome and
+ then by start position (e.g., ``sort -k1,1 -k2,2n in.bed > in.sorted.bed``
+ for BED files).
+
+.. seealso::
+
+ :doc:`../tools/cluster`
+ :doc:`../tools/complement`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools merge [OPTIONS] -i <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ mergeBed [OPTIONS] -i <BED/GFF/VCF>
+
+
+
+=========================== ===============================================================================================================================================================================================================
+Option Description
+=========================== ===============================================================================================================================================================================================================
+**-s** Force strandedness. That is, only merge features that are the same strand. *By default, this is disabled*.
+**-n** Report the number of BED entries that were merged. *1 is reported if no merging occurred*.
+**-d** Maximum distance between features allowed for features to be merged. *Default is 0. That is, overlapping and/or book-ended features are merged*.
+**-nms** Report the names of the merged features separated by commas. Change delimiter with ``-delim``
+
+**-scores** | Report the scores of the merged features.
+ | Specify one of the following options for reporting scores:
+ | ``sum``, ``min``, ``max``,
+ | ``mean``, ``median``, ``mode``, ``antimode``,
+ | ``collapse`` (i.e., print a semicolon-separated list)
+
+**-delim** | Specify a custom delimiter for the -nms and -scores concat options
+ | Example: ``-delim "|"``
+ | ``Default: ";"``
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or
+bookended intervals into a single, "flattened" or "merged" interval.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 180 250
+ chr1 250 500
+ chr1 501 1000
+
+ $ bedtools merge -i A.bed
+ chr1 100 500
+ chr1 501 1000
+
+
+==========================================================================
+``-s`` Enforcing "strandedness"
+==========================================================================
+The ``-s`` option will only merge intervals that are overlapping/bookended
+*and* are on the same strand.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+ chr1 180 250 a2 2 +
+ chr1 250 500 a3 3 -
+ chr1 501 1000 a4 4 +
+
+ $ bedtools merge -i A.bed -s
+ chr1 100 250 +
+ chr1 501 1000 +
+ chr1 250 500 -
+
+
+
+==========================================================================
+``-n`` Reporting the number of features that were merged
+==========================================================================
+The -n option will report the number of features that were combined from the
+original file in order to make the newly merged feature. If a feature in the
+original file was not merged with any other features, a "1" is reported.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 180 250
+ chr1 250 500
+ chr1 501 1000
+
+ $ bedtools merge -i A.bed -n
+ chr1 100 500 3
+ chr1 501 1000 1
+
+
+==========================================================================
+``-d`` Controlling how close two features must be in order to merge
+==========================================================================
+By default, only overlapping or book-ended features are combined into a new
+feature. However, one can force ``merge`` to combine more distant features
+with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
+features that overlap or are within 1000 base pairs of one another will be
+combined.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+ chr1 501 1000
+
+ $ bedtools merge -i A.bed
+ chr1 100 200
+ chr1 501 1000
+
+ $ bedtools merge -i A.bed -d 1000
+ chr1 100 200 1000
+
+
+==========================================================================
+``-nms`` Reporting the names of the features that were merged
+==========================================================================
+Occasionally, one might like to know that names of the features that were
+merged into a new feature. The ``-nms`` option will add an extra column to the
+``merge`` output which lists (separated by semicolons) the names of the
+merged features.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 A1
+ chr1 150 300 A2
+ chr1 250 500 A3
+
+ $ bedtools merge -i A.bed -nms
+ chr1 100 500 A1,A2,A3
+
+
+==========================================================================
+``-scores`` Reporting the scores of the features that were merged
+==========================================================================
+Similarly, we might like to know that scores of the features that were
+merged into a new feature. Enter the ``-scores`` option. One can specify
+how the scores from each overlapping interval should be reported.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 A1 1
+ chr1 150 300 A2 2
+ chr1 250 500 A3 3
+
+ $ bedtools merge -i A.bed -scores mean
+ chr1 100 500 2
+
+ $ bedtools merge -i A.bed -scores max
+ chr1 100 500 3
+
+ $ bedtools merge -i A.bed -scores collapse
+ chr1 100 500 1,2,3
+
+
+==========================================================================
+``-delim`` Change the delimiter for ``-nms`` and ``-scores collapse``
+==========================================================================
+One can override the use of a comma as the delimiter for the ``-nms`` and
+``-scores collapse`` options via the use of the ``-delim`` option.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 A1
+ chr1 150 300 A2
+ chr1 250 500 A3
+
+Compare:
+
+.. code-block:: bash
+
+ $ bedtools merge -i A.bed -nms
+ chr1 100 500 A1,A2,A3
+
+to:
+
+.. code-block:: bash
+
+ $ bedtools merge -i A.bed -nms -delim "|"
+ chr1 100 500 A1|A2|A3
diff --git a/docs/content/tools/multicov.rst b/docs/content/tools/multicov.rst
new file mode 100644
index 0000000..160461b
--- /dev/null
+++ b/docs/content/tools/multicov.rst
@@ -0,0 +1,98 @@
+.. _multicov:
+
+###############
+*multicov*
+###############
+``bedtools multicov``, reports the count of alignments from multiple
+position-sorted and indexed BAM files that overlap intervals in a BED file.
+Specifically, for each BED interval provided, it reports a separate count of
+overlapping alignments from each BAM file.
+
+.. note::
+
+ ``bedtools multicov`` depends upon index BAM files in order to count the
+ number of overlaps in each BAM file. As such, each BAM file should be
+ position sorted (``samtool sort aln.bam aln.sort``) and
+ indexed (``samtools index aln.sort.bam``) with either samtools or bamtools.
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools multicov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ multiBamCov [OPTIONS] -bams BAM1 BAM2 BAM3 ... BAMn -bed <BED/GFF/VCF>
+
+
+============ ================================================================
+ Option Description
+============ ================================================================
+**-split** Treat "split" BAM or BED12 entries as distinct BED intervals.
+**-s** Require same strandedness. That is, only report hits in B
+ that overlap A on the _same_ strand. By default, overlaps are
+ reported without respect to strand.
+**-S** Require different strandedness. That is, only report hits in B
+ that overlap A on the _opposite_ strand. By default, overlaps
+ are reported without respect to strand.
+**-f** Minimum overlap required as a fraction of each A. Default is
+ 1E-9 (i.e., 1bp).
+**-r** Require that the fraction overlap be reciprocal for A and B. In
+ other words, if -f is 0.90 and -r is used, this requires that
+ B overlap 90% of A and A _also_ overlaps 90% of B.
+**-q** Minimum mapping quality (MAPQ) allowed. Default is 0.
+**-D** Include duplicate reads. Default counts non-duplicates only
+**-F** Include failed-QC reads. Default counts pass-QC reads only
+**-p** Only count proper pairs. Default counts all alignments with
+ ``MAPQ > -q`` argument, regardless of the BAM FLAG field.
+============ ================================================================
+
+
+==========================================================================
+Default behavior.
+==========================================================================
+By default, ``multicov`` will report the count of alignments in each input
+BAM file that overlap.
+
+.. code-block:: bash
+
+ $ cat ivls-of-interest.bed
+ chr1 0 10000 ivl1
+ chr1 10000 20000 ivl2
+ chr1 20000 30000 ivl3
+ chr1 30000 40000 ivl4
+
+ $ bedtools multicov -bams aln1.bam aln2.bam aln3.bam -bed ivls-of-interest.bed
+ chr1 0 10000 ivl1 100 2234 0
+ chr1 10000 20000 ivl2 123 3245 1000
+ chr1 20000 30000 ivl3 213 2332 2034
+ chr1 30000 40000 ivl4 335 7654 0
+
+
+The output of ``multicov`` reflects a distinct report of the overlapping
+alignments for each record in the ``-bed`` file. In the example above, each
+line of the output reflects **a)** the original line from the ``-bed`` file
+followed by **b)** the count of alignments that overlap the ``-bed`` interval
+from each input ``-bam`` file. In the example above, the output consists of
+7 columns: the first four of which are the columns from the ``-bed`` file and
+the last 3 are the count of overlapping alignments from the 3 input ``-bam``
+files. The order of the counts reflects the order of the files given on the
+command line.
+
+.. note::
+
+ ``bedtools multicov`` will work with a single BAM as well.
+
+.. code-block:: bash
+
+ $ bedtools multicov -bams aln1.bam -bed ivls-of-interest.bed
+ chr1 0 10000 ivl1 100
+ chr1 10000 20000 ivl2 123
+ chr1 20000 30000 ivl3 213
+ chr1 30000 40000 ivl4 335
+
diff --git a/docs/content/tools/multiinter.rst b/docs/content/tools/multiinter.rst
new file mode 100644
index 0000000..87cbc6b
--- /dev/null
+++ b/docs/content/tools/multiinter.rst
@@ -0,0 +1,5 @@
+.. _multiinter:
+
+###############
+*multiinter*
+###############
diff --git a/docs/content/tools/nuc.rst b/docs/content/tools/nuc.rst
new file mode 100644
index 0000000..fabe575
--- /dev/null
+++ b/docs/content/tools/nuc.rst
@@ -0,0 +1,5 @@
+.. _nuc:
+
+###############
+*nuc*
+###############
diff --git a/docs/content/overlap.rst b/docs/content/tools/overlap.rst
similarity index 97%
rename from docs/content/overlap.rst
rename to docs/content/tools/overlap.rst
index 418c4c8..f365ead 100755
--- a/docs/content/overlap.rst
+++ b/docs/content/tools/overlap.rst
@@ -1,5 +1,7 @@
+.. _overlap:
+
###############
-5.19 overlap
+*overlap*
###############
**overlap** computes the amount of overlap (in the case of positive values) or distance (in the case of
negative values) between feature coordinates occurring on the same input line and reports the result at
@@ -7,9 +9,10 @@ the end of the same line. In this way, it is a useful method for computing custo
the output of other BEDTools.
==========================================================================
-5.19.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
overlap [OPTIONS] -i <input> -cols s1,e1,s2,e2
@@ -23,10 +26,11 @@ Usage:
==========================================================================
-5.19.2 Default behavior
+Default behavior
==========================================================================
The default behavior is to compute the amount of overlap between the features you specify based on the
start and end coordinates. For example:
+
::
windowBed -a A.bed -b B.bed -w 10
chr1 10 20 A chr1 15 25 B
@@ -34,6 +38,7 @@ start and end coordinates. For example:
# Now let's say we want to compute the number of base pairs of overlap
# between the overlapping features from the output of windowBed.
+
::
windowBed -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7
chr1 10 20 A chr1 15 25 B 5
diff --git a/docs/content/tools/pairtobed.rst b/docs/content/tools/pairtobed.rst
new file mode 100644
index 0000000..e872c91
--- /dev/null
+++ b/docs/content/tools/pairtobed.rst
@@ -0,0 +1,5 @@
+.. _pairtobed:
+
+###############
+*pairtobed*
+###############
diff --git a/docs/content/pairToPair.rst b/docs/content/tools/pairtopair.rst
similarity index 96%
rename from docs/content/pairToPair.rst
rename to docs/content/tools/pairtopair.rst
index 7be6819..c4645a8 100755
--- a/docs/content/pairToPair.rst
+++ b/docs/content/tools/pairtopair.rst
@@ -1,5 +1,7 @@
+.. _pairtopair:
+
###############
-5.3 pairToPair
+*pairtopair*
###############
**pairToPair** compares two BEDPE files in search of overlaps where each end of a BEDPE feature in A
overlaps with the ends of a feature in B. For example, using pairToPair, one could screen for the exact
@@ -8,9 +10,10 @@ discordant pair suggests the same structural variation in each file/sample.
================================
-5.3.1 Usage and option summary
+Usage and option summary
================================
**Usage:**
+
::
pairToPair [OPTIONS] -a <BEDPE> -b <BEDPE>
@@ -37,7 +40,7 @@ Option Description
================================
-5.3.2 Default behavior
+Default behavior
================================
By default, a BEDPE feature from A will be reported if *both* ends overlap a feature in the BEDPE B
file. If strand information is present for the two BEDPE files, it will be further required that the
@@ -45,6 +48,7 @@ overlaps on each end be on the same strand. This way, an otherwise overlapping (
locations) F/R alignment will not be matched with a R/R alignment.
Default: Report A if *both* ends overlaps B.
+
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -57,6 +61,7 @@ Default: Report A if *both* ends overlaps B.
Default when strand information is present in both BEDPE files: Report A if *both* ends overlaps B *on
the same strands*.
+
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -77,12 +82,13 @@ the same strands*.
==================================================
-5.3.3 (-type neither)Optional overlap requirements
+``-type neither`` Optional overlap requirements
==================================================
Using then **-type neither, pairToPair** will only report A if *neither* end overlaps with a BEDPE
feature in B.
**-type neither**: Report A only if *neither* end overlaps B.
+
::
Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -100,4 +106,4 @@ feature in B.
Result =====.................................=====
-
\ No newline at end of file
+
diff --git a/docs/content/tools/random.rst b/docs/content/tools/random.rst
new file mode 100644
index 0000000..680d150
--- /dev/null
+++ b/docs/content/tools/random.rst
@@ -0,0 +1,157 @@
+.. _random:
+
+###############
+*random*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/random-glyph.png
+ :width: 600pt
+|
+
+`bedtools random` will generate a random set of intervals in BED6 format. One
+can specify both the number (``-n``) and the size (``-l``) of the intervals
+that should be generated.
+
+
+.. seealso::
+
+ :doc:`../tools/shuffle`
+ :doc:`../tools/jaccard`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+
+::
+
+ bedtools random [OPTIONS] -g <GENOME>
+
+**(or)**:
+:
+:
+
+ randomBed [OPTIONS] -g <GENOME>
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-l** | The length of the intervals to generate.
+ | ``Default = 100``
+
+**-n** | The number of intervals to generate.
+ | ``Default = 1,000,000``
+
+**-seed** Supply an integer seed for the shuffling. This will allow feature shuffling experiments to be recreated exactly as the seed for the pseudo-random number generation will be constant. *By default, the seed is chosen automatically*.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, `bedtools random` generate 1 million intervals of length 100
+placed randomly in the genome specificed with ``-g``.
+
+.. code-block:: bash
+
+ $ bedtools random -g hg19.genome
+ chr2 87536758 87536858 1 100 -
+ chrX 46051735 46051835 2 100 +
+ chr18 5237041 5237141 3 100 -
+ chr12 45809998 45810098 4 100 +
+ chrX 42034890 42034990 5 100 -
+ chr10 77510935 77511035 6 100 -
+ chr3 39844278 39844378 7 100 -
+ chr6 101012700 101012800 8 100 +
+ chr12 38123482 38123582 9 100 +
+ chr7 88508598 88508698 10 100 -
+
+ $ bedtools random -g hg19.genome
+ chr3 141987850 141987950 1 100 +
+ chr5 137643331 137643431 2 100 +
+ chr2 155523858 155523958 3 100 -
+ chr5 147874094 147874194 4 100 +
+ chr1 71838335 71838435 5 100 -
+ chr8 71154323 71154423 6 100 -
+ chr2 133240474 133240574 7 100 +
+ chr9 131495427 131495527 8 100 +
+ chrX 125952943 125953043 9 100 +
+ chr3 59685545 59685645 10 100 +
+
+
+==========================================================================
+``-n`` Specify the *number* of intervals to generate.
+==========================================================================
+The `-n` option allows one to override the default of generating 1 million
+intervals.
+
+.. code-block:: bash
+
+ $ bedtools random -g hg19.genome -n 3
+ chr20 47975280 47975380 1 100 -
+ chr16 23381222 23381322 2 100 +
+ chr3 104913816 104913916 3 100 -
+
+
+==========================================================================
+``-l`` Specify the *length* of intervals to generate.
+==========================================================================
+The `-l` option allows one to override the default interval length of 100bp.
+
+.. code-block:: bash
+
+ $ bedtools random -g hg19.genome -l 5
+ chr9 54133731 54133736 1 5 +
+ chr1 235288830 235288835 2 5 -
+ chr8 26744718 26744723 3 5 +
+ chr3 187313616 187313621 4 5 -
+ chr11 88996846 88996851 5 5 -
+ chr13 84714855 84714860 6 5 -
+ chr13 10759738 10759743 7 5 -
+ chr6 122569739 122569744 8 5 +
+ chr17 50884025 50884030 9 5 -
+ chr11 38576901 38576906 10 5 +
+
+
+==========================================================================
+``-seed`` Defining a "seed" for the random interval creation.
+==========================================================================
+`bedtools random` uses a pseudo-random number generator to permute the
+locations of BED features. Therefore, each run should produce a different
+result. This can be problematic if one wants to exactly recreate an experiment.
+By using the `seed` option, one can supply a custom integer seed for
+`bedtools random`. In turn, each execution of `bedtools random` with the same
+seed and input files should produce identical results.
+
+.. code-block:: bash
+
+ $ bedtools random -g hg19.genome -seed 71346
+ chrY 23380696 23380796 1 100 -
+ chr14 94368315 94368415 2 100 +
+ chr14 45353323 45353423 3 100 -
+ chr14 100546766 100546866 4 100 -
+ chr12 43294368 43294468 5 100 -
+ chr1 141470585 141470685 6 100 -
+ chr10 31273665 31273765 7 100 +
+ chr5 19102979 19103079 8 100 +
+ chr3 116730634 116730734 9 100 -
+ chr3 101222965 101223065 10 100 -
+
+ # (same seed, thus same as above)
+ $ bedtools random -g hg19.genome -seed 71346
+ chrY 23380696 23380796 1 100 -
+ chr14 94368315 94368415 2 100 +
+ chr14 45353323 45353423 3 100 -
+ chr14 100546766 100546866 4 100 -
+ chr12 43294368 43294468 5 100 -
+ chr1 141470585 141470685 6 100 -
+ chr10 31273665 31273765 7 100 +
+ chr5 19102979 19103079 8 100 +
+ chr3 116730634 116730734 9 100 -
+ chr3 101222965 101223065 10 100 -
+
diff --git a/docs/content/tools/reldist.rst b/docs/content/tools/reldist.rst
new file mode 100644
index 0000000..c269828
--- /dev/null
+++ b/docs/content/tools/reldist.rst
@@ -0,0 +1,197 @@
+.. _reldist:
+
+###############
+*reldist*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/reldist-glyph.png
+ :width: 600pt
+
+Traditional approaches to summarizing the similarity between two sets of genomic intervals
+are based upon the number or proportion of *intersecting* intervals. However, such measures
+are largely blind to spatial correlations between the two sets where, dpesite consistent spacing
+or proximity, intersections are rare (for example, enhancers and transcription start sites rarely overlap,
+yet they are much closer to one another than two sets of random intervals). Favorov et al [1] proposed
+a *relative distance* metric that describes distribution of relative distances between each interval in
+one set nd the two closest intervals in another set (see figure above). If there is no spatial
+correlation between the two sets, one would expect the relative distances to be uniformaly distributed
+among the relative distances ranging from 0 to 0.5. If, however, the intervals tend to be much closer than expected
+by chance, the distribution of observed relative distances would be shifted towards low relative distance values (e.g., the figure below).
+
+.. image:: ../images/tool-glyphs/reldist-plot.png
+ :width: 600pt
+
+
+.. code::
+
+ [1] Exploring Massive, Genome Scale Datasets with the GenometriCorr Package.
+ Favorov A, Mularoni L, Cope LM, Medvedeva Y, Mironov AA, et al. (2012)
+ PLoS Comput Biol 8(5): e1002529. doi:10.1371/journal.pcbi.1002529
+
+
+.. seealso::
+
+ :doc:`../tools/jaccard`
+ :doc:`../tools/closest`
+
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools reldist [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+
+=========================== =========================================================================================================================================================
+Option Description
+=========================== =========================================================================================================================================================
+**-a** BED/GFF/VCF file A. Each feature in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe.
+**-b** BED/GFF/VCF file B. Use "stdin" if passing B with a UNIX pipe.
+**-detail** Instead of a summary, report the relative distance for each interval in A
+=========================== =========================================================================================================================================================
+
+
+===============================
+Default behavior
+===============================
+By default, ``bedtools reldist`` reports the distribution of relative distances between two sets of intervals.
+The output reports the frequency of each relative distance (ranging from 0.0 to 0.5). If the two sets of intervals
+are randomly distributed with respect to one another, eahc relative distance "bin" with be roughly equally represented
+(i.e., a uniform distribution). For example, consider the relative distance distance distribution for exons and AluY
+elements:
+
+.. code-block:: bash
+
+
+ $ bedtools reldist \
+ -a data/refseq.chr1.exons.bed.gz \
+ -b data/
+ aluY.chr1.bed.gz
+ 0.00 164 43408 0.004
+ 0.01 551 43408 0.013
+ 0.02 598 43408 0.014
+ 0.03 637 43408 0.015
+ 0.04 793 43408 0.018
+ 0.05 688 43408 0.016
+ 0.06 874 43408 0.020
+ 0.07 765 43408 0.018
+ 0.08 685 43408 0.016
+ 0.09 929 43408 0.021
+ 0.10 876 43408 0.020
+ 0.11 959 43408 0.022
+ 0.12 860 43408 0.020
+ 0.13 851 43408 0.020
+ 0.14 903 43408 0.021
+ 0.15 893 43408 0.021
+ 0.16 883 43408 0.020
+ 0.17 828 43408 0.019
+ 0.18 917 43408 0.021
+ 0.19 875 43408 0.020
+ 0.20 897 43408 0.021
+ 0.21 986 43408 0.023
+ 0.22 903 43408 0.021
+ 0.23 944 43408 0.022
+ 0.24 904 43408 0.021
+ 0.25 867 43408 0.020
+ 0.26 943 43408 0.022
+ 0.27 933 43408 0.021
+ 0.28 1132 43408 0.026
+ 0.29 881 43408 0.020
+ 0.30 851 43408 0.020
+ 0.31 963 43408 0.022
+ 0.32 950 43408 0.022
+ 0.33 965 43408 0.022
+ 0.34 907 43408 0.021
+ 0.35 884 43408 0.020
+ 0.36 965 43408 0.022
+ 0.37 944 43408 0.022
+ 0.38 911 43408 0.021
+ 0.39 939 43408 0.022
+ 0.40 921 43408 0.021
+ 0.41 950 43408 0.022
+ 0.42 935 43408 0.022
+ 0.43 919 43408 0.021
+ 0.44 915 43408 0.021
+ 0.45 934 43408 0.022
+ 0.46 843 43408 0.019
+ 0.47 850 43408 0.020
+ 0.48 1006 43408 0.023
+ 0.49 937 43408 0.022
+
+In contrast, consider the relative distance distribution observed between exons and conserved elements:
+
+.. code-block:: bash
+
+ $ bedtools reldist \
+ -a data/refseq.chr1.exons.bed.gz \
+ -b data/gerp.chr1.bed.gz
+ reldist count total fraction
+ 0.00 20629 43422 0.475
+ 0.01 2629 43422 0.061
+ 0.02 1427 43422 0.033
+ 0.03 985 43422 0.023
+ 0.04 897 43422 0.021
+ 0.05 756 43422 0.017
+ 0.06 667 43422 0.015
+ 0.07 557 43422 0.013
+ 0.08 603 43422 0.014
+ 0.09 487 43422 0.011
+ 0.10 461 43422 0.011
+ 0.11 423 43422 0.010
+ 0.12 427 43422 0.010
+ 0.13 435 43422 0.010
+ 0.14 375 43422 0.009
+ 0.15 367 43422 0.008
+ 0.16 379 43422 0.009
+ 0.17 371 43422 0.009
+ 0.18 346 43422 0.008
+ 0.19 389 43422 0.009
+ 0.20 377 43422 0.009
+ 0.21 411 43422 0.009
+ 0.22 377 43422 0.009
+ 0.23 352 43422 0.008
+ 0.24 334 43422 0.008
+ 0.25 315 43422 0.007
+ 0.26 370 43422 0.009
+ 0.27 330 43422 0.008
+ 0.28 330 43422 0.008
+ 0.29 280 43422 0.006
+ 0.30 309 43422 0.007
+ 0.31 326 43422 0.008
+ 0.32 287 43422 0.007
+ 0.33 294 43422 0.007
+ 0.34 306 43422 0.007
+ 0.35 307 43422 0.007
+ 0.36 309 43422 0.007
+ 0.37 271 43422 0.006
+ 0.38 293 43422 0.007
+ 0.39 311 43422 0.007
+ 0.40 331 43422 0.008
+ 0.41 320 43422 0.007
+ 0.42 299 43422 0.007
+ 0.43 327 43422 0.008
+ 0.44 321 43422 0.007
+ 0.45 326 43422 0.008
+ 0.46 306 43422 0.007
+ 0.47 354 43422 0.008
+ 0.48 365 43422 0.008
+ 0.49 336 43422 0.008
+ 0.50 38 43422 0.001
+
+
+Moreover, if one compares the relative distances for one set against itself, every interval
+should be expected to overlap an interval in the other set (itself). As such, the relative
+distances will all be 0.0:
+
+.. code-block:: bash
+
+ $ bedtools reldist \
+ -a data/refseq.chr1.exons.bed.gz \
+ -b data/refseq.chr1.exons.bed.gz
+ reldist count total fraction
+ 0.00 43424 43424 1.000
+
diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst
new file mode 100755
index 0000000..d846e5c
--- /dev/null
+++ b/docs/content/tools/shuffle.rst
@@ -0,0 +1,232 @@
+.. _shuffle:
+
+###############
+*shuffle*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/shuffle-glyph.png
+ :width: 600pt
+
+
+`bedtools shuffle` will randomly permute the genomic locations of a feature
+file among a genome defined in a genome file. One can also provide an
+"exclusions" BED/GFF/VCF file that lists regions where you do
+not want the permuted features to be placed. For example, one might want to
+prevent features from being placed in known genome gaps. `shuffle` is useful
+as a *null* basis against which to test the significance of associations
+of one feature with another.
+
+
+.. seealso::
+
+ :doc:`../tools/random`
+ :doc:`../tools/jaccard`
+
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools shuffle [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
+
+**(or)**:
+::
+
+ shuffleBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME>
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-excl** A BED file of coordinates in which features from -i should *not* be placed (e.g., genome gaps).
+**-incl** A BED file of coordinates in which features from -i *should* be placed.
+**-chrom** Keep features in -i on the same chromosome. Solely permute their location on the chromosome. *By default, both the chromosome and position are randomly chosen*.
+**-seed** Supply an integer seed for the shuffling. This will allow feature shuffling experiments to be recreated exactly as the seed for the pseudo-random number generation will be constant. *By default, the seed is chosen automatically*.
+**-f** Maximum overlap (as a fraction of the ``-i`` feature) with an ``-excl`` feature that is tolerated before searching for a new, randomized locus.
+**-chromFirst** Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size.
+**-bedpe** Indicate that the A file is in BEDPE format.
+**-maxTries** Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl. *Default = 1000.*
+**-noOverlapping** Don't allow shuffled intervals to overlap.
+**-allowBeyondChromEnd** Allow the original the length of the original records to extebd beyond the length of the chromosome.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, `bedtools shuffle` will reposition each feature in the input BED
+file on a random chromosome at a random position. The size and strand of each
+feature are preserved.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 0 100 a1 1 +
+ chr1 0 1000 a2 2 -
+
+ $ cat my.genome
+ chr1 10000
+ chr2 8000
+ chr3 5000
+ chr4 2000
+
+ $ bedtools shuffle -i A.bed -g my.genome
+ chr4 1498 1598 a1 1 +
+ chr3 2156 3156 a2 2 -
+
+
+
+
+
+==========================================================================
+``-chrom`` Requiring that features be shuffled on the same chromosome
+==========================================================================
+The `-chrom` option behaves the same as the default behavior except that
+features are randomly placed on the same chromosome as defined in the BED file.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 0 100 a1 1 +
+ chr1 0 1000 a2 2 -
+
+ $ cat my.genome
+ chr1 10000
+ chr2 8000
+ chr3 5000
+ chr4 2000
+
+ $ bedtools shuffle -i A.bed -g my.genome -chrom
+ chr1 9560 9660 a1 1 +
+ chr1 7258 8258 a2 2 -
+
+
+
+
+==========================================================================
+``-excl`` Excluding certain genome regions from ``bedtools shuffle``
+==========================================================================
+One may want to prevent BED features from being placed in certain regions of
+the genome. For example, one may want to exclude genome gaps from permutation
+experiment. The `excl` option defines a BED file of regions that should be
+excluded. ``bedtools shuffle`` will attempt to permute the locations of all features
+while adhering to the exclusion rules. However it will stop looking for an
+appropriate location if it cannot find a valid spot for a feature
+after 1,000,000 tries.
+
+For example (*note that the exclude file excludes all but 100 base pairs of the chromosome*):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 0 100 a1 1 +
+ chr1 0 1000 a2 2 -
+
+ $ cat my.genome
+ chr1 10000
+
+ $ cat exclude.bed
+ chr1 100 10000
+
+ $ bedtools shuffle -i A.bed -g my.genome -excl exclude.bed
+ chr1 0 100 a1 1 +
+ Error, line 2: tried 1000000 potential loci for entry, but could not avoid excluded
+ regions. Ignoring entry and moving on.
+
+
+For example (*now the exclusion file only excludes the first 100 bases of the chromosome*):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 0 100 a1 1 +
+ chr1 0 1000 a2 2 -
+
+ $ cat my.genome
+ chr1 10000
+
+ $ cat exclude.bed
+ chr1 0 100
+
+ $ bedtools shuffle -i A.bed -g my.genome -excl exclude.bed
+ chr1 147 247 a1 1 +
+ chr1 2441 3441 a2 2 -
+
+
+==========================================================================
+``-seed`` Defining a "seed" for the random replacement.
+==========================================================================
+`bedtools shuffle` uses a pseudo-random number generator to permute the
+locations of BED features. Therefore, each run should produce a different
+result. This can be problematic if one wants to exactly recreate an experiment.
+By using the `seed` option, one can supply a custom integer seed for
+`bedtools shuffle`. In turn, each execution of `bedtools shuffle` with the same
+seed and input files should produce identical results.
+
+For example (*note that the exclude file below excludes all but 100 base pairs
+of the chromosome*):
+
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 0 100 a1 1 +
+ chr1 0 1000 a2 2 -
+
+ $ cat my.genome
+ chr1 10000
+
+ $ bedtools shuffle -i A.bed -g my.genome -seed 927442958
+ chr1 6177 6277 a1 1 +
+ chr1 8119 9119 a2 2 -
+
+ $ bedtools shuffle -i A.bed -g my.genome -seed 927442958
+ chr1 6177 6277 a1 1 +
+ chr1 8119 9119 a2 2 -
+
+ . . .
+
+ $ bedtools shuffle -i A.bed -g my.genome -seed 927442958
+ chr1 6177 6277 a1 1 +
+ chr1 8119 9119 a2 2 -
+
+==========================================================================
+``-noOverlapping`` Prevent shuffled intervals from overlapping.
+==========================================================================
+There often arise cases where one wants to shuffle intervals throughout
+the genome, yet one wants to prevent the intervals from occupying a single
+common base pair. The ``-noOverlapping`` option allows one to enforce
+no such overlaps.
+
+.. code-block:: bash
+
+ $ bedtools shuffle -i A.bed -g my.genome -noOverlapping
+
+
+==========================================================================
+``-allowBeyondChromEnd`` Allow records to extend beyond the chrom. length.
+==========================================================================
+By default, ``shuffle`` requires that an interval's original length must be
+fully-contained within the chromosome. Yet there are cases where you might
+want to allow shuffled intervals to be relocated to a position
+in which the entire original interval cannot fit w/o exceeding
+the end of the chromosome. By using the ``-noOverlapping`` option,
+``shuffle`` will allow intervals to be shuffled to locations that are so close
+to the chromosome end that the full length of the original record cannot
+be contained within the chromosome length. In such cases, the end coordinate
+for the shuffled interval will be set (i.e., truncated)
+to the chromosome's length.
+
+.. code-block:: bash
+
+ $ bedtools shuffle -i A.bed -g my.genome -allowBeyondChromEnd
+
+
+
diff --git a/docs/content/tools/slop.rst b/docs/content/tools/slop.rst
new file mode 100755
index 0000000..fb4b9ae
--- /dev/null
+++ b/docs/content/tools/slop.rst
@@ -0,0 +1,147 @@
+.. _slop:
+
+###############
+*slop*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/slop-glyph.png
+ :width: 600pt
+
+|
+
+``bedtools slop`` will increase the size of each feature in a feature file by a
+user-defined number of bases. While something like this could be done with an
+``awk '{OFS="\t" print $1,$2-<slop>,$3+<slop>}'``,
+``bedtools slop`` will restrict the resizing to the size of the chromosome
+(i.e. no start < 0 and no end > chromosome size).
+
+.. note::
+
+ In order to prevent the extension of intervals beyond chromosome boundaries,
+ ``bedtools slop`` requires a *genome* file defining the length of each
+ chromosome or contig.
+
+.. seealso::
+
+ :doc:`../tools/flank`
+
+==========================================================================
+Usage and option summary
+==========================================================================
+**Usage**:
+::
+
+ bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+**(or):**
+::
+
+ slopBed [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
+
+=========================== ===============================================================================================================================================================================================================
+ Option Description
+=========================== ===============================================================================================================================================================================================================
+**-b** Increase the BED/GFF/VCF entry by the same number base pairs in each direction. *Integer*.
+**-l** The number of base pairs to subtract from the start coordinate. *Integer*.
+**-r** The number of base pairs to add to the end coordinate. *Integer*.
+**-s** Define -l and -r based on strand. For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the *end* coordinate.
+**-pct** Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.
+**-header** Print the header from the input file prior to results.
+=========================== ===============================================================================================================================================================================================================
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools slop`` will either add a fixed number of bases in each
+direction (``-b``) or an asymmetric number of bases in each direction
+with ``-l`` and ``-r``.
+
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 5 100
+ chr1 800 980
+
+ $ cat my.genome
+ chr1 1000
+
+ $ bedtools slop -i A.bed -g my.genome -b 5
+ chr1 0 105
+ chr1 795 985
+
+ $ bedtools slop -i A.bed -g my.genome -l 2 -r 3
+ chr1 3 103
+ chr1 798 983
+
+
+However, if the requested number of bases exceeds the boundaries of the
+chromosome, ``bedtools slop`` will "clip" the feature accordingly.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 5 100
+ chr1 800 980
+
+ $ cat my.genome
+ chr1 1000
+
+ $ bedtools slop -i A.bed -g my.genome -b 5000
+ chr1 0 1000
+ chr1 0 1000
+
+
+
+==========================================================================
+``-s`` Resizing features according to strand
+==========================================================================
+``bedtools slop`` will optionally increase the size of a feature based on strand.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+ chr1 100 200 a2 2 -
+
+ $ cat my.genome
+ chr1 1000
+
+ $ bedtools slop -i A.bed -g my.genome -l 50 -r 80 -s
+ chr1 50 280 a1 1 +
+ chr1 20 250 a2 2 -
+
+
+==========================================================================
+``-pct`` Resizing features by a given fraction
+==========================================================================
+``bedtools slop`` will optionally increase the size of a feature by a
+user-specific fraction.
+
+For example:
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+
+ $ bedtools slop -i A.bed -g my.genome -b 0.5 -pct
+ chr1 50 250 a1 1 +
+
+ $ bedtools slop -i a.bed -l 0.5 -r 0.0 -pct -g my.genome
+ chr1 50 200 a1 1 +
+
+
+==========================================================================
+``-header`` Print the header for the A file before reporting results.
+==========================================================================
+By default, if your A file has a header, it is ignored when reporting results.
+This option will instead tell bedtools to first print the header for the
+A file prior to reporting results.
+
diff --git a/docs/content/sortBed.rst b/docs/content/tools/sort.rst
similarity index 95%
rename from docs/content/sortBed.rst
rename to docs/content/tools/sort.rst
index 7ea1666..05a4e3a 100755
--- a/docs/content/sortBed.rst
+++ b/docs/content/tools/sort.rst
@@ -1,12 +1,15 @@
+.. _sort:
+
###############
-5.15 sortBed
+*sort*
###############
**sortBed** sorts a feature file by chromosome and other criteria.
==========================================================================
-5.15.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
sortBed [OPTIONS] -i <BED/GFF/VCF>
@@ -24,11 +27,12 @@ Usage:
==========================================================================
-5.15.2 Default behavior
+Default behavior
==========================================================================
By default, **sortBed** sorts a BED file by chromosome and then by start position in ascending order.
For example:
+
::
cat A.bed
chr1 800 1000
@@ -46,11 +50,12 @@ For example:
==========================================================================
-5.15.3 Optional sorting behavior
+Optional sorting behavior
==========================================================================
**sortBed** will also sorts a BED file by chromosome and then by other criteria.
For example, to sort by chromosome and then by feature size (in descending order):
+
::
cat A.bed
chr1 800 1000
@@ -68,8 +73,9 @@ For example, to sort by chromosome and then by feature size (in descending order
**Disclaimer:** it should be noted that **sortBed** is merely a convenience utility, as the UNIX sort utility
will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
by chromosome then by start position in the following manner:
+
::
- sort -k 1,1 -k2,2 -n a.bed
+ sort -k 1,1 -k2,2n a.bed
chr1 1 10
chr1 80 180
chr1 750 10000
diff --git a/docs/content/tools/subtract.rst b/docs/content/tools/subtract.rst
new file mode 100755
index 0000000..6b1d808
--- /dev/null
+++ b/docs/content/tools/subtract.rst
@@ -0,0 +1,157 @@
+.. _subtract:
+
+###############
+*subtract*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/subtract-glyph.png
+ :width: 600pt
+
+|
+
+``bedtools subtract`` searches for features in B that overlap A. If an
+overlapping feature is found in B, the overlapping portion is removed from A
+and the remaining portion of A is reported. If a feature in B overlaps all of a
+feature in A, the A feature will not be reported.
+
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools subtract [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ subtractBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
+
+
+
+=========================== ===============================================================================================================================================================================================================
+Option Description
+=========================== ===============================================================================================================================================================================================================
+**-f** Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp).
+**-s** Force "strandedness". That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand.
+**-S** Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
+**-A** Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or ``-f`` amount), the entire feature is removed.
+**-N** Same as -A except when used with -f, the amount is the sum of all features (not any single feature).
+=========================== ===============================================================================================================================================================================================================
+
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools subtracts`` removes each overlapping interval in B
+from A. If a feature in B *completely* overlaps a feature in A, the A feature
+is removed.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10 20
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 0 30
+ chr1 180 300
+
+ $ bedtools subtract -a A.bed -b B.bed
+ chr1 100 180
+
+
+
+
+
+
+==========================================================================
+``-f`` Requiring a minimal overlap fraction before subtracting
+==========================================================================
+This option behaves the same as the ``-f`` option for ``bedtools intersect``.
+In this case, ``subtract`` will only subtract an overlap with B if it covers at
+least the fraction of A defined by ``-f``. If an overlap is found,
+but it does not meet the overlap fraction, the original A feature is
+reported without subtraction.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 180 300
+
+ $ bedtools subtract -a A.bed -b B.bed -f 0.10
+ chr1 100 180
+
+ $ bedtools subtract -a A.bed -b B.bed -f 0.80
+ chr1 100 200
+
+
+
+
+==========================================================================
+``-s`` Enforcing same "strandedness"
+==========================================================================
+This option behaves the same as the ``-s`` option for ``bedtools intersect``
+while scanning for features in B that should be subtracted from A.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+
+ $ cat B.bed
+ chr1 80 120 b1 1 +
+ chr1 180 300 b2 1 -
+
+ $ bedtools subtract -a A.bed -b B.bed -s
+ chr1 120 200 a1 1 +
+
+
+==========================================================================
+``-S`` Enforcing opposite "strandedness"
+==========================================================================
+This option behaves the same as the ``-s`` option for ``bedtools intersect``
+while scanning for features in B that should be subtracted from A.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200 a1 1 +
+
+ $ cat B.bed
+ chr1 80 120 b1 1 +
+ chr1 180 300 b2 1 -
+
+ $ bedtools subtract -a A.bed -b B.bed -S
+ chr1 100 180 a1 1 +
+
+
+==========================================================================
+``-A`` Remove features with any overlap
+==========================================================================
+Unlike the default behavior, the ``-A`` option will completely remove
+a feature from A if it has even 1bp of overlap with a feature in B.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 180 300
+
+ $ bedtools subtract -a A.bed -b B.bed
+ chr1 100 180
+
+ $ bedtools subtract -a A.bed -b B.bed -A
+
+
+
+
diff --git a/docs/content/tools/tag.rst b/docs/content/tools/tag.rst
new file mode 100644
index 0000000..6793032
--- /dev/null
+++ b/docs/content/tools/tag.rst
@@ -0,0 +1,5 @@
+.. _tag:
+
+###############
+*tag*
+###############
diff --git a/docs/content/unionBedGraphs.rst b/docs/content/tools/unionbedg.rst
similarity index 93%
rename from docs/content/unionBedGraphs.rst
rename to docs/content/tools/unionbedg.rst
index b1e34a1..41ce91f 100755
--- a/docs/content/unionBedGraphs.rst
+++ b/docs/content/tools/unionbedg.rst
@@ -1,14 +1,17 @@
+.. _unionbedg:
+
###############
-5.23 unionBedGraphs
+*unionbedg*
###############
**unionBedGraphs** combines multiple BEDGRAPH files into a single file such that one can directly
compare coverage (and other text-values such as genotypes) across multiple sample
==========================================================================
-5.23.1 Usage and option summary
+Usage and option summary
==========================================================================
Usage:
+
::
unionBedGraphs [OPTIONS] -i FILE1 FILE2 FILE3 ... FILEn
@@ -28,9 +31,10 @@ Usage:
==========================================================================
-5.23.2 Default behavior
+Default behavior
==========================================================================
Figure:
+
::
cat 1.bg
chr1 1000 1500 10
@@ -59,9 +63,10 @@ Figure:
chr1 2090 2100 20 0 20
==========================================================================
-5.23.3 Add a header line to the output
+``-header`` Add a header line to the output
==========================================================================
Figure:
+
::
unionBedGraphs -i 1.bg 2.bg 3.bg -header
chrom start end 1 2 3
@@ -77,9 +82,10 @@ Figure:
==========================================================================
-5.23.4 Add a header line with custom file names to the output
+``-names`` Add a header line with custom file names to the output
==========================================================================
Figure:
+
::
unionBedGraphs -i 1.bg 2.bg 3.bg -header -names WT-1 WT-2 KO-1
chrom start end WT-1 WT-2 KO-1
@@ -97,9 +103,10 @@ Figure:
==========================================================================
-5.23.5 Include regions that have zero coverage in all BEDGRAPH files.
+``-empty`` Include regions that have zero coverage in all BEDGRAPH files.
==========================================================================
Figure:
+
::
unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header
chrom start end WT-1 WT-2 KO-1
@@ -119,9 +126,10 @@ Figure:
==========================================================================
-5.23.6 Use a custom value for missing values.
+``-filler`` Use a custom value for missing values.
==========================================================================
Figure:
+
::
unionBedGraphs -i 1.bg 2.bg 3.bg -empty -g sizes.txt -header -filler N/A
chrom start end WT-1 WT-2 KO-1
@@ -141,9 +149,10 @@ Figure:
==========================================================================
-5.23.7 Use BEDGRAPH files with non-numeric values.
+Use BEDGRAPH files with non-numeric values.
==========================================================================
Figure:
+
::
cat 1.snp.bg
chr1 0 1 A/G
@@ -160,4 +169,4 @@ Figure:
unionBedGraphs -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/-
chr1 0 1 A/G C/C A/G
chr1 5 6 C/T -/- C/T
- chr1 7 8 -/- T/T -/-
\ No newline at end of file
+ chr1 7 8 -/- T/T -/-
diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst
new file mode 100755
index 0000000..850180f
--- /dev/null
+++ b/docs/content/tools/window.rst
@@ -0,0 +1,210 @@
+.. _window:
+
+###############
+*window*
+###############
+
+|
+
+.. image:: ../images/tool-glyphs/window-glyph.png
+ :width: 600pt
+
+|
+
+Similar to ``bedtools intersect``, ``window`` searches for overlapping features
+in A and B. However, ``window`` adds a specified number (1000, by default) of
+base pairs upstream and downstream of each feature in A. In effect, this allows
+features in B that are "near" features in A to be detected.
+
+===============================
+Usage and option summary
+===============================
+**Usage**:
+::
+
+ bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>
+
+**(or)**:
+::
+
+ bedtools window [OPTIONS] [-a|-abam] -b <BED/GFF/VCF>
+
+
+
+=========================== =========================================================================================================================================================
+Option Description
+=========================== =========================================================================================================================================================
+**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | bedtools window -abam stdin -b genes.bed
+**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
+**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: bedtools window -abam reads.bam -b genes.bed -bed
+**-w** Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. *Default is 1000 bp*.
+**-l** Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
+**-r** Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
+**-sw** Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. *By default, this is disabled*.
+**-sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
+**-Sm** Only report hits in B that overlap A on the opposite strand. *By default, overlaps are reported without respect to strand*.
+**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.
+**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B.
+**-v** Only report those entries in A that have *no overlaps* with B.
+**-header** Print the header from the A file prior to results.
+=========================== =========================================================================================================================================================
+
+
+==========================================================================
+Default behavior
+==========================================================================
+By default, ``bedtools window`` adds 1000 bp upstream and downstream of each A
+feature and searches for features in B that overlap this "window". If an overlap
+is found in B, both the *original* A feature and the *original* B feature are
+reported.
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 500 1000
+ chr1 1300 2000
+
+ $ bedtools window -a A.bed -b B.bed
+ chr1 100 200 chr1 500 1000
+
+
+==========================================================================
+``-w`` Defining a custom window size
+==========================================================================
+Instead of using the default window size of 1000bp, one can define a custom,
+*symmetric* window around each feature in A using the **-w** option. One should
+specify the window size in base pairs. For example, a window of 5kb should be
+defined as ``-w 5000``.
+
+For example (note that in contrast to the default behavior,
+the second B entry is reported):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 100 200
+
+ $ cat B.bed
+ chr1 500 1000
+ chr1 1300 2000
+
+ $ bedtools window -a A.bed -b B.bed -w 5000
+ chr1 100 200 chr1 500 1000
+ chr1 100 200 chr1 1300 2000
+
+
+==========================================================================
+``-l and -r`` Defining *assymteric* windows
+==========================================================================
+One can also define asymmetric windows where a differing number of bases are
+added upstream and downstream of each feature using the ``-l`` (upstream)
+and ``-r`` (downstream)** options.
+
+.. note::
+
+ By default, the ``-l`` and ``-r`` options ignore strand. If you want to define
+ *upstream* and *downstream* based on strand, use the ``-sw`` option (below)
+ with the ``-l`` and ``-r`` options.
+
+For example (note the difference between -l 200 and -l 300):
+
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 1000 2000
+
+ $ cat B.bed
+ chr1 500 800
+ chr1 10000 20000
+
+ $ bedtools window -a A.bed -b B.bed -l 200 -r 20000
+ chr1 1000 2000 chr1 10000 20000
+
+ $ bedtools window -a A.bed -b B.bed -l 300 -r 20000
+ chr1 1000 2000 chr1 500 800
+ chr1 1000 2000 chr1 10000 20000
+
+
+==========================================================================
+``-sw`` Defining assymteric windows based on strand
+==========================================================================
+Especially when dealing with gene annotations or RNA-seq experiments, you may
+want to define asymmetric windows based on "strand". For example, you may want
+to screen for overlaps that occur within 5000 bp upstream of a gene (e.g. a
+promoter region) while screening only 1000 bp downstream of the gene.
+By enabling the ``-sw`` ("stranded" windows) option, the windows are added
+upstream or downstream according to strand. For example, imagine one
+specifies ``-l 5000``, ``-r 1000`` as well as the ``-sw`` option. In this case,
+forward stranded ("+") features will screen 5000 bp to the *left* (that is,
+*lower* genomic coordinates) and 1000 bp to the *right* (that is, *higher*
+genomic coordinates). By contrast, reverse stranded ("-") features will screen
+5000 bp to the *right* (that is, *higher* genomic coordinates) and 1000 bp to
+the *left* (that is, *lower* genomic coordinates).
+
+For example (note the difference between ``-l 200`` and ``-l 300``):
+
+.. code-block:: bash
+
+ $ cat A.bed
+ chr1 10000 20000 A.forward 1 +
+ chr1 10000 20000 A.reverse 1 -
+
+ $ cat B.bed
+ chr1 1000 8000 B1
+ chr1 24000 32000 B2
+
+ $ bedtools window -a A.bed -b B.bed -l 5000 -r 1000 -sw
+ chr1 10000 20000 A.forward 1 + chr1 1000 8000 B1
+ chr1 10000 20000 A.reverse 1 - chr1 24000 32000 B2
+
+
+
+==========================================================================
+``-sm`` Enforcing matches with the *same* "strandedness"
+==========================================================================
+This option behaves the same as the ``-s`` option for ``bedtools intersect``
+while scanning for overlaps within the "window" surrounding A. That is, overlaps
+in B will only be included if the B interval is on the *same* strand as the A
+interval.
+
+==========================================================================
+``-Sm`` Enforcing matches with the *opposite* "strandedness"
+==========================================================================
+This option behaves the same as the ``-S`` option for ``bedtools intersect`` while
+scanning for overlaps within the "window" surrounding A. That is, overlaps in
+B will only be included if the B interval is on the *opposite* strand as the A
+interval.
+
+
+==========================================================================
+``-u`` Reporting the presence/absence of at least one overlapping feature
+==========================================================================
+This option behaves the same as for ``bedtools intersect``. That is, even if
+multiple overlaps exist, each A interval will only be reported once.
+
+
+==========================================================================
+``-c`` Reporting the number of overlapping features
+==========================================================================
+This option behaves the same as for ``bedtools intersect``. That is, it will
+report the *count* of intervals in B that overlap each A interval.
+
+
+
+==========================================================================
+``-v`` Reporting the absence of any overlapping features
+==========================================================================
+This option behaves the same as for ``bedtools intersect``. That is, it will
+only report those intervals in A that have have *zero* overlaps in B.
+
+
+==========================================================================
+``-header`` Print the header for the A file before reporting results.
+==========================================================================
+By default, if your A file has a header, it is ignored when reporting results.
+This option will instead tell bedtools to first print the header for the
+A file prior to reporting results.
diff --git a/docs/content/windowBed.rst b/docs/content/windowBed.rst
deleted file mode 100755
index 30d231e..0000000
--- a/docs/content/windowBed.rst
+++ /dev/null
@@ -1,157 +0,0 @@
-###############
-5.5 windowBed
-###############
-
-Similar to **intersectBed**, **windowBed** searches for overlapping features in A and B. However,
-**windowBed** adds a specified number (1000, by default) of base pairs upstream and downstream of
-each feature in A. In effect, this allows features in B that are "near" features in A to be detected.
-
-==========================================================================
-5.5.1 Usage and option summary
-==========================================================================
-**Usage:**
-::
- windowBed [OPTIONS] -a <BED/GFF/VCF> -b <BED/GFF/VCF>
-
-
-=========================== =========================================================================================================================================================
-Option Description
-=========================== =========================================================================================================================================================
-**-abam** BAM file A. Each BAM alignment in A is compared to B in search of overlaps. Use "stdin" if passing A with a UNIX pipe: For example: samtools view -b <BAM> | windowBed -abam stdin -b genes.bed
-**-ubam** Write uncompressed BAM output. The default is write compressed BAM output.
-**-bed** When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam. For example: windowBed -abam reads.bam -b genes.bed -bed
-**-w** Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. *Default is 1000 bp*.
-**-l** Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
-**-r** Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. *Allows one to create assymetrical "windows". Default is 1000bp*.
-**-sw** Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. *By default, this is disabled*.
-**-sm** Only report hits in B that overlap A on the same strand. *By default, overlaps are reported without respect to strand*.
-**-u** Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B.
-**-c** For each entry in A, report the number of hits in B while restricting to -f. Reports 0 for A entries that have no overlap with B.
-=========================== =========================================================================================================================================================
-
-==========================================================================
-5.5.2 Default behavior
-==========================================================================
-By default, **windowBed** adds 1000 bp upstream and downstream of each A feature and searches for
-features in B that overlap this "window". If an overlap is found in B, both the *original* A feature and the
-*original* B feature are reported. For example, in the figure below, feature B1 would be found, but B2
-would not.
-::
- Chromosome ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- "window" = 10
- BED File A <----------*************---------->
-
- BED File B ^^^^^^^^ ^^^^^^
-
- Result ========
-
-For example:
-::
- cat A.bed
- chr1 100 200
-
- cat B.bed
- chr1 500 1000
- chr1 1300 2000
-
- windowBed -a A.bed -b B.bed
- chr1 100 200 chr1 500 1000
-
-
-==========================================================================
-5.5.3 (-w)Defining a custom window size
-==========================================================================
-Instead of using the default window size of 1000bp, one can define a custom, *symmetric* window around
-each feature in A using the **-w** option. One should specify the window size in base pairs. For example,
-a window of 5kb should be defined as **-w 5000**.
-
-For example (note that in contrast to the default behavior, the second B entry is reported):
-::
- cat A.bed
- chr1 100 200
-
- cat B.bed
- chr1 500 1000
- chr1 1300 2000
-
- windowBed -a A.bed -b B.bed -w 5000
- chr1 100 200 chr1 500 1000
- chr1 100 200 chr1 1300 2000
-
-==========================================================================
-5.5.4 (-l and -r)Defining assymteric windows
-==========================================================================
-One can also define asymmetric windows where a differing number of bases are added upstream and
-downstream of each feature using the **-l (upstream)** and **-r (downstream)** options.
-
-For example (note the difference between -l 200 and -l 300):
-::
- cat A.bed
- chr1 1000 2000
-
- cat B.bed
- chr1 500 800
- chr1 10000 20000
-
- windowBed -a A.bed -b B.bed -l 200 -r 20000
- chr1 100 200 chr1 10000 20000
-
- windowBed -a A.bed -b B.bed -l 300 -r 20000
- chr1 100 200 chr1 500 800
- chr1 100 200 chr1 10000 20000
-
-==========================================================================
-5.5.5 (-sw)Defining assymteric windows based on strand
-==========================================================================
-Especially when dealing with gene annotations or RNA-seq experiments, you may want to define
-asymmetric windows based on "strand". For example, you may want to screen for overlaps that occur
-within 5000 bp upstream of a gene (e.g. a promoter region) while screening only 1000 bp downstream of
-the gene. By enabling the **-sw** ("stranded" windows) option, the windows are added upstream or
-downstream according to strand. For example, imagine one specifies **-l 5000 -r 1000** as well as the **-
-sw** option. In this case, forward stranded ("+") features will screen 5000 bp to the *left* (that is, *lower*
-genomic coordinates) and 1000 bp to the *right* (that is, *higher* genomic coordinates). By contrast,
-reverse stranded ("-") features will screen 5000 bp to the *right* (that is, *higher* genomic coordinates) and
-1000 bp to the *left* (that is, *lower* genomic coordinates).
-
-For example (note the difference between -l 200 and -l 300):
-::
- cat A.bed
- chr1 10000 20000 A.forward 1 +
- chr1 10000 20000 A.reverse 1 -
-
- cat B.bed
- chr1 1000 8000 B1
- chr1 24000 32000 B2
-
- windowBed -a A.bed -b B.bed -l 5000 -r 1000 -sw
- chr1 10000 20000 A.forward 1 + chr1 1000 8000 B1
- chr1 10000 20000 A.reverse 1 - chr1 24000 32000 B2
-
-
-
-==========================================================================
-5.5.6 (-sm)Enforcing "strandedness"
-==========================================================================
-This option behaves the same as the -s option for intersectBed while scanning for overlaps within the
-"window" surrounding A. See the discussion in the intersectBed section for details.
-
-==========================================================================
-5.5.7 (-u)Reporting the presence of at least one overlapping feature
-==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
-
-
-==========================================================================
-5.5.8 (-c)Reporting the number of overlapping features
-==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
-
-
-==========================================================================
-5.5.9 (-v)Reporting the absence of any overlapping features
-==========================================================================
-This option behaves the same as for intersectBed while scanning for overlaps within the "window"
-surrounding A. See the discussion in the intersectBed section for details.
-
diff --git a/docs/index.rst b/docs/index.rst
index 0ed8165..c10368a 100755
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -2,18 +2,23 @@
**bedtools**: *a powerful toolset for genome arithmetic*
================================================================
-=================
-Overview
-=================
-
-Brief paragraph of the software.
+Collectively, the **bedtools** utilities are a swiss-army knife of tools
+for a wide-range of genomics analysis tasks. The most widely-used
+tools enable *genome arithmetic*: that is, set theory on the genome. For
+example, **bedtools** allows one to *intersect*, *merge*, *count*, *complement*,
+and *shuffle* genomic intervals from multiple files in widely-used
+genomic file formats such as BAM, BED, GFF/GTF, VCF.
+While each individual tool is designed to do a relatively simple task (e.g.,
+*intersect* two interval files), quite sophisticated analyses can be conducted
+by combining multiple bedtools operations on the UNIX command line.
=================
Table of contents
=================
.. toctree::
:maxdepth: 1
+ :numbered:
content/overview
content/installation
@@ -22,10 +27,88 @@ Table of contents
content/bedtools-suite
content/example-usage
content/advanced-usage
+ content/tips-and-tricks
+ content/faq
+ content/related-tools
+
+
+=================
+Performance
+=================
+As of version 2.18, ``bedtools`` is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are pre-sorted
+by chromosome and start position. As you can see in the plots below, the speed and memory consumption scale nicely
+with sorted data as compared to the poor scaling for unsorted data. The current version of bedtools intersect is as fast as (or slightly faster) than the ``bedops`` package's ``bedmap`` which uses a similar algorithm for sorted data. The plots below represent counting the number of intersecting alignments from exome capture BAM files against CCDS exons.
+The alignments have been converted to BED to facilitate comparisons to ``bedops``. We compare to the bedmap ``--ec`` option because similar error checking is enforced by ``bedtools``.
+
+Note: bedtools could not complete when using 100 million alignments and the R-Tree algorithm used for unsorted data owing to a lack of memory.
+
+.. image:: content/images/speed-comparo.png
+ :width: 300pt
+.. image:: content/images/memory-comparo.png
+ :width: 300pt
+
+Commands used:
+
+.. code-block:: bash
+
+ # bedtools sorted
+ $ bedtools intersect \
+ -a ccds.exons.bed -b aln.bam.bed \
+ -c \
+ -sorted
+
+ # bedtools unsorted
+ $ bedtools intersect \
+ -a ccds.exons.bed -b aln.bam.bed \
+ -c
+
+ # bedmap (without error checking)
+ $ bedmap --echo --count --bp-ovr 1 \
+ ccds.exons.bed aln.bam.bed
+
+ # bedmap (no error checking)
+ $ bedmap --ec --echo --count --bp-ovr 1 \
+ ccds.exons.bed aln.bam.bed
+
+
+
+=================
+Brief example
+=================
+Let's imagine you have a BED file of ChiP-seq peaks from two different
+experiments. You want to identify peaks that were observed in *both* experiments
+(requiring 50% reciprocal overlap) and for those peaks, you want to find to
+find the closest, non-overlapping gene. Such an analysis could be conducted
+with two, relatively simple bedtools commands.
+
+.. code-block:: bash
+
+ # intersect the peaks from both experiments.
+ # -f 0.50 combined with -r requires 50% reciprocal overlap between the
+ # peaks from each experiment.
+ $ bedtools intersect -a exp1.bed -b exp2.bed -f 0.50 -r > both.bed
+
+ # find the closest, non-overlapping gene for each interval where
+ # both experiments had a peak
+ # -io ignores overlapping intervals and returns only the closest,
+ # non-overlapping interval (in this case, genes)
+ $ bedtools closest -a both.bed -b genes.bed -io > both.nearest.genes.txt
+
+==========
+License
+==========
+bedtools is freely available under a GNU Public License (Version 2).
+
+=====================================
+Acknowledgments
+=====================================
+To do.
+
=================
Mailing list
=================
-Refer to the mailing list.
+If you have questions, requests, or bugs to report, please email the
+`bedtools mailing list <https://groups.google.com/forum/?fromgroups#!forum/bedtools-discuss>`_
diff --git a/docs/templates/page.html b/docs/templates/page.html
new file mode 100644
index 0000000..4e1e3cb
--- /dev/null
+++ b/docs/templates/page.html
@@ -0,0 +1,140 @@
+{% extends "!page.html" %}
+
+{% set google_analytics_id = 'UA-37270821-1' %}
+{% set disqus_shortname = 'bedtoolsdocs' %}
+
+{# note, currently these must be set... #}
+{% set github_base_account = 'arq5x' %}
+{% set github_project = 'bedtools' %}
+
+{##################################################}
+{# for plone-derived "edit me" & Google analytics #}
+{##################################################}
+
+{% block footer %}
+{{ super() }}
+
+{# Add plone-derived 'edit me' sticky note #}
+<div id="editor-trap">
+ <h3>Edit and improve this document!</h3>
+
+ <p>
+ This file can be edited directly through the Web. Anyone can
+ update and fix errors in this document with few clicks --
+ no downloads needed.
+ <p>
+
+ <ol>
+
+ <li>
+ Go to
+ <a href="https://github.com/{{ github_base_account }}/{{ github_project }}/blob/master/docs/{{ pagename }}.rst">
+ {{ title }}
+ </a> on GitHub.
+ </li>
+
+ <li>
+ <b>Edit</b> files using GitHub's text editor in your web browser (see the 'Edit' tab on the top right of the file)
+ </li>
+
+ <li>
+ Fill in the <b>Commit message</b> text box at the bottom of the page describing <i>why</i>
+ you made the changes. Press the <b>Propose file change</b> button next to it when done.
+ </li>
+
+ <li>
+ Then click <b>Send a pull request</b>.
+ </li>
+
+ <li>
+ Your changes are now queued for review under the project's <a href="https://github.com/{{ github_base_account }}/{{ github_project }}/pulls">Pull requests</a> tab on GitHub!
+ </li>
+ </ol>
+
+ <p>
+ For an introduction to the documentation format please see <a href="http://docutils.sourceforge.net/docs/user/rst/quickstart.html">the reST primer</a>.
+ </p>
+
+ </div>
+
+<script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', {{ google_analytics_id }}]);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+</script>
+
+{% endblock %}
+
+{#########################}
+{# for disqus commenting #}
+{#########################}
+
+{% macro comments() %}
+
+<div id="disqus_thread"></div>
+<script type="text/javascript">
+ /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
+ var disqus_shortname = '{{ disqus_shortname }}'; // required: replace example with your forum shortname
+
+ /* * * DON'T EDIT BELOW THIS LINE * * */
+ (function() {
+ var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
+ dsq.src = 'http://' + disqus_shortname + '.disqus.com/embed.js';
+ (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
+ })();
+</script>
+<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
+<a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a>
+
+{% endmacro %}
+
+{% block extrahead %}
+
+{% if github_base_account %}
+<script src="{{ pathto('_static/labibi.js', 1) }}"></script>
+{% else %}
+<style type="text/css">
+<!-- github-based editing disabled; set github_base_account
+ and github_project -->
+#editor-trap.toggled {
+ display: none;
+}
+</style>
+{% endif %}
+
+{% if google_analytics_id %}
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', '']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+{% else %}
+<!-- Google Analytics JS is disabled; set google_analytics_id -->
+{% endif %}
+{% endblock %}
+
+{%- block body %}
+ {{ super() }}
+
+{% if disqus_shortname %}
+ {{ comments() }}
+{% else %}
+<!-- disqus commenting disabled; set disqus_shortname -->
+{% endif %}
+
+{%- endblock %}
+
diff --git a/docs/templates/sidebar-intro.html b/docs/templates/sidebar-intro.html
new file mode 100644
index 0000000..ed9f59c
--- /dev/null
+++ b/docs/templates/sidebar-intro.html
@@ -0,0 +1,22 @@
+<p>
+ Bedtools is a fast, flexible toolset for genome arithmetic.
+</p>
+<h3>Bedtools links</h3>
+<ul>
+ <li><a target="_blank" href="https://github.com/arq5x/bedtools/issues">Issue Tracker</a></li>
+ <li><a target="_blank" href="https://github.com/arq5x/bedtools">Source @ GitHub</a></li>
+ <li><a target="_blank" href="https://bedtools.googlecode.com">Releases @ Google Code</a></li>
+ <li><a target="_blank" href="http://groups.google.com/group/bedtools-discuss">Mailing list @ Google Groups</a></li>
+ <li><a target="_blank" href="http://www.biostars.org/show/tag/bedtools/">Queries @ Biostar</a></li>
+ <li><a target="_blank" href="http://quinlanlab.org">Quinlan lab @ UVa</a></li>
+
+</ul>
+
+<h3>Sources</h3>
+<p><a href="https://github.com/arq5x/bedtools">Browse source @ GitHub</a>.</p>
+
+<h3>Releases</h3>
+<ul>
+ <li><a href="https://github.com/arq5x/bedtools2/releases">Stable releasees now @ Github</a></li>
+</ul>
+
diff --git a/docs/themes/rtd/static/rtd.css_t b/docs/themes/rtd/static/rtd.css_t
index 66736c0..4302d93 100755
--- a/docs/themes/rtd/static/rtd.css_t
+++ b/docs/themes/rtd/static/rtd.css_t
@@ -525,6 +525,9 @@ div.warning p.admonition-title {
}
+
+
+
/* Sidebars only */
div.sidebar {
max-width: 200px;
diff --git a/src/annotateBed/annotateBed.cpp b/src/annotateBed/annotateBed.cpp
index 40d7ef4..8b7e301 100644
--- a/src/annotateBed/annotateBed.cpp
+++ b/src/annotateBed/annotateBed.cpp
@@ -189,11 +189,14 @@ void BedAnnotate::ReportAnnotations() {
int nonZeroBases = (length - zeroDepthCount);
float fractCovered = (float) nonZeroBases / length;
if (_reportCounts == false && _reportBoth == false)
- printf("%f\t", fractCovered);
+ printf("%f", fractCovered);
else if (_reportCounts == true && _reportBoth == false)
- printf("%d\t", bedItr->counts[i]);
+ printf("%d", bedItr->counts[i]);
else if (_reportCounts == false && _reportBoth == true)
- printf("%d\t%f\t", bedItr->counts[i], fractCovered);
+ printf("%d\t%f", bedItr->counts[i], fractCovered);
+
+ if (i != _annoFiles.size() - 1)
+ printf("\t");
}
// print newline for next feature.
printf("\n");
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index f7d7304..16d6164 100644
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -38,25 +38,28 @@ void bamtobed_help(void);
void ConvertBamToBed(const string &bamFile, bool useEditDistance,
const string &bamTag, bool writeBed12,
- bool obeySplits, const string &color,
- bool useCigar, bool useNovoalign,
- bool useBWA);
+ bool obeySplits, bool splitOnDeletions,
+ const string &color, bool useCigar,
+ bool useNovoalign, bool useBWA);
-void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance);
+void ConvertBamToBedpe(const string &bamFile,
+ const bool &useEditDistance, bool mate1First);
string PrintTag(const BamAlignment &bam, const string &tag);
void PrintBed(const BamAlignment &bam, const RefVector &refs,
bool useEditDistance, const string &bamTag,
- bool obeySplits, bool useCigar,
- bool useNovoalign, bool useBWA);
+ bool obeySplits, bool splitOnDeletions,
+ bool useCigar, bool useNovoalign,
+ bool useBWA);
void PrintBed12(const BamAlignment &bam, const RefVector &refs,
- bool useEditDistance, const string &bamTag,
+ bool useEditDistance, const string &bamTag,
+ bool obeySplits, bool splitOnDeletions,
string color = "255,0,0");
void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2,
- const RefVector &refs, bool useEditDistance);
+ const RefVector &refs, bool useEditDistance, bool mate1First);
void ParseCigarBed12(const vector<CigarOp> &cigar, vector<int> &blockStarts,
vector<int> &blockEnds, int &alignmentEnd);
@@ -85,6 +88,8 @@ int bamtobed_main(int argc, char* argv[]) {
bool useAlignmentScore = false;
bool useCigar = false;
bool obeySplits = false;
+ bool splitOnDeletions = false;
+ bool mate1First = false;
bool useNovoalign = false; // custom for Quinlan/Hall research
bool useBWA = false; // custom for Quinlan/Hall research
@@ -113,29 +118,36 @@ int bamtobed_main(int argc, char* argv[]) {
}
}
else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
- writeBedPE = true;
+ writeBedPE = true;
}
else if(PARAMETER_CHECK("-bed12", 6, parameterLength)) {
- writeBed12 = true;
+ writeBed12 = true;
}
else if(PARAMETER_CHECK("-split", 6, parameterLength)) {
- obeySplits = true;
+ obeySplits = true;
+ }
+ else if(PARAMETER_CHECK("-splitD", 7, parameterLength)) {
+ obeySplits = true;
+ splitOnDeletions = true;
}
else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
- useEditDistance = true;
- tag = "NM";
+ useEditDistance = true;
+ tag = "NM";
}
else if(PARAMETER_CHECK("-cigar", 6, parameterLength)) {
- useCigar = true;
+ useCigar = true;
}
else if(PARAMETER_CHECK("-as", 3, parameterLength)) {
- useAlignmentScore = true;
+ useAlignmentScore = true;
}
else if(PARAMETER_CHECK("-novo", 5, parameterLength)) {
- useNovoalign = true;
+ useNovoalign = true;
}
else if(PARAMETER_CHECK("-bwa", 4, parameterLength)) {
- useBWA = true;
+ useBWA = true;
+ }
+ else if(PARAMETER_CHECK("-mate1", 6, parameterLength)) {
+ mate1First = true;
}
else if(PARAMETER_CHECK("-color", 6, parameterLength)) {
if ((i+1) < argc) {
@@ -194,15 +206,22 @@ int bamtobed_main(int argc, char* argv[]) {
<< "*****" << endl;
showHelp = true;
}
+ if (writeBedPE == false && mate1First == true) {
+ cerr << endl << "*****" << endl
+ << "*****ERROR: Must use -mate1 with -bedpe." << endl
+ << "*****" << endl;
+ showHelp = true;
+ }
// if there are no problems, let's convert BAM to BED or BEDPE
if (!showHelp) {
if (writeBedPE == false)
ConvertBamToBed(bamFile, useEditDistance,
tag, writeBed12,
- obeySplits, color,
- useCigar, useNovoalign, useBWA);
+ obeySplits, splitOnDeletions,
+ color, useCigar,
+ useNovoalign, useBWA);
else
- ConvertBamToBedpe(bamFile, useEditDistance);
+ ConvertBamToBedpe(bamFile, useEditDistance, mate1First);
}
else {
bamtobed_help();
@@ -221,29 +240,36 @@ void bamtobed_help(void) {
cerr << "Options: " << endl;
- cerr << "\t-bedpe\t" << "Write BEDPE format." << endl;
- cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
-
- cerr << "\t-bed12\t" << "Write \"blocked\" BED format (aka \"BED12\")." << endl << endl;
- cerr << "\t\thttp://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1" << endl << endl;
-
- cerr << "\t-split\t" << "Report \"split\" BAM alignments as separate BED entries." << endl << endl;
-
- cerr << "\t-ed\t" << "Use BAM edit distance (NM tag) for BED score." << endl;
- cerr << "\t\t- Default for BED is to use mapping quality." << endl;
- cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
- cerr << "\t\t the two mapping qualities for the pair." << endl;
- cerr << "\t\t- When -ed is used with -bedpe, the total edit" << endl;
- cerr << "\t\t distance from the two mates is reported." << endl << endl;
-
- cerr << "\t-tag\t" << "Use other NUMERIC BAM alignment tag for BED score." << endl;
- cerr << "\t\t- Default for BED is to use mapping quality." << endl;
- cerr << "\t\t Disallowed with BEDPE output." << endl << endl;
-
- cerr << "\t-color\t" << "An R,G,B string for the color used with BED12 format." << endl;
- cerr << "\t\tDefault is (255,0,0)." << endl << endl;
-
- cerr << "\t-cigar\t" << "Add the CIGAR string to the BED entry as a 7th column." << endl << endl;
+ cerr << "\t-bedpe\t" << "Write BEDPE format." << endl;
+ cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
+
+ cerr << "\t-mate1\t" << "When writing BEDPE (-bedpe) format, " << endl;
+ cerr << "\t\talways report mate one as the first BEDPE \"block\"." << endl << endl;
+
+ cerr << "\t-bed12\t" << "Write \"blocked\" BED format (aka \"BED12\"). Forces -split." << endl << endl;
+ cerr << "\t\thttp://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1" << endl << endl;
+
+ cerr << "\t-split\t" << "Report \"split\" BAM alignments as separate BED entries." << endl ;
+ cerr << "\t\tSplits only on N CIGAR operations." << endl << endl;
+
+ cerr << "\t-splitD\t" << "Split alignments based on N and D CIGAR operators." << endl;
+ cerr << "\t\tForces -split." << endl << endl;
+
+ cerr << "\t-ed\t" << "Use BAM edit distance (NM tag) for BED score." << endl;
+ cerr << "\t\t- Default for BED is to use mapping quality." << endl;
+ cerr << "\t\t- Default for BEDPE is to use the minimum of" << endl;
+ cerr << "\t\t the two mapping qualities for the pair." << endl;
+ cerr << "\t\t- When -ed is used with -bedpe, the total edit" << endl;
+ cerr << "\t\t distance from the two mates is reported." << endl << endl;
+
+ cerr << "\t-tag\t" << "Use other NUMERIC BAM alignment tag for BED score." << endl;
+ cerr << "\t\t- Default for BED is to use mapping quality." << endl;
+ cerr << "\t\t Disallowed with BEDPE output." << endl << endl;
+
+ cerr << "\t-color\t" << "An R,G,B string for the color used with BED12 format." << endl;
+ cerr << "\t\tDefault is (255,0,0)." << endl << endl;
+
+ cerr << "\t-cigar\t" << "Add the CIGAR string to the BED entry as a 7th column." << endl << endl;
// end the program here
@@ -252,8 +278,10 @@ void bamtobed_help(void) {
void ConvertBamToBed(const string &bamFile, bool useEditDistance, const string &bamTag,
- bool writeBed12, bool obeySplits, const string &color,
- bool useCigar, bool useNovoalign, bool useBWA) {
+ bool writeBed12, bool obeySplits, bool splitOnDeletions,
+ const string &color, bool useCigar, bool useNovoalign, bool useBWA)
+{
+
// open the BAM file
BamReader reader;
if (!reader.Open(bamFile)) {
@@ -270,9 +298,11 @@ void ConvertBamToBed(const string &bamFile, bool useEditDistance, const string &
while (reader.GetNextAlignment(bam)) {
if (bam.IsMapped() == true) {
if (writeBed12 == false) // BED
- PrintBed(bam, refs, useEditDistance, bamTag, obeySplits, useCigar, useNovoalign, useBWA);
+ PrintBed(bam, refs, useEditDistance, bamTag, obeySplits, splitOnDeletions,
+ useCigar, useNovoalign, useBWA);
else //"blocked" BED
- PrintBed12(bam, refs, useEditDistance, bamTag, color);
+ PrintBed12(bam, refs, useEditDistance, bamTag, obeySplits, splitOnDeletions,
+ color);
}
}
reader.Close();
@@ -284,7 +314,10 @@ void ConvertBamToBed(const string &bamFile, bool useEditDistance, const string &
1. The BAM file is grouped/sorted by query name,
not alignment position
*/
-void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance) {
+void ConvertBamToBedpe(const string &bamFile,
+ const bool &useEditDistance,
+ bool mate1First)
+{
// open the BAM file
BamReader reader;
if (!reader.Open(bamFile)) {
@@ -313,10 +346,10 @@ void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance) {
bam1 = bam2;
reader.GetNextAlignment(bam2);
}
- PrintBedPE(bam1, bam2, refs, useEditDistance);
+ PrintBedPE(bam1, bam2, refs, useEditDistance, mate1First);
}
else if (bam1.IsPaired() && bam2.IsPaired()) {
- PrintBedPE(bam1, bam2, refs, useEditDistance);
+ PrintBedPE(bam1, bam2, refs, useEditDistance, mate1First);
}
}
reader.Close();
@@ -361,8 +394,9 @@ string PrintTag(const BamAlignment &bam, const string &tag)
void PrintBed(const BamAlignment &bam, const RefVector &refs,
bool useEditDistance, const string &bamTag,
- bool obeySplits, bool useCigar,
- bool useNovoalign, bool useBWA)
+ bool obeySplits, bool splitOnDeletions,
+ bool useCigar, bool useNovoalign,
+ bool useBWA)
{
// set the strand
string strand = "+";
@@ -456,24 +490,45 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs,
vector<BED> bedBlocks;
string chrom = refs.at(bam.RefID).RefName;
// extract the block starts and lengths from the CIGAR string
- GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ if (!splitOnDeletions)
+ GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ else
+ GetBamBlocks(bam, chrom, bedBlocks, true, true);
+
unsigned int i;
for (i = 0; i < bedBlocks.size(); ++i) {
BED curr = bedBlocks[i];
- printf("%s\t%d\t%d\t\%s\t%d\t%s\n",
- chrom.c_str(),
- curr.start,
- curr.end,
- name.c_str(),
- bam.MapQuality,
- strand.c_str());
+
+ if (bamTag == "") {
+ printf("%s\t%d\t%d\t%s\t%d\t%s\n",
+ chrom.c_str(),
+ curr.start,
+ curr.end,
+ name.c_str(),
+ bam.MapQuality,
+ strand.c_str());
+ }
+ else {
+ cout << chrom << "\t"
+ << bam.Position << "\t"
+ << curr.start << "\t"
+ << curr.end << "\t"
+ << name << "\t"
+ << PrintTag(bam, bamTag) << "\t"
+ << strand
+ << endl;
+ }
}
}
}
-void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, const string &bamTag, string color) {
+void PrintBed12(const BamAlignment &bam, const RefVector &refs,
+ bool useEditDistance, const string &bamTag,
+ bool obeySplits, bool splitOnDeletions,
+ string color)
+{
// set the strand
string strand = "+";
@@ -489,7 +544,10 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
string chrom = refs.at(bam.RefID).RefName;
CHRPOS alignmentEnd = bam.GetEndPosition();
// extract the block starts and lengths from the CIGAR string
- GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ if (!splitOnDeletions)
+ GetBamBlocks(bam, chrom, bedBlocks, false, true);
+ else
+ GetBamBlocks(bam, chrom, bedBlocks, true, true);
if (bamTag == "") {
cout << refs.at(bam.RefID).RefName << "\t"
@@ -527,7 +585,8 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
}
-void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, bool useEditDistance) {
+void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2,
+ const RefVector &refs, bool useEditDistance, bool mate1First) {
// initialize BEDPE variables
string chrom1, chrom2, strand1, strand2;
@@ -575,11 +634,24 @@ void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVec
}
// swap the ends if necessary
- if ( chrom1 > chrom2 || ((chrom1 == chrom2) && (start1 > start2)) ) {
- swap(chrom1, chrom2);
- swap(start1, start2);
- swap(end1, end2);
- swap(strand1, strand2);
+ if (!mate1First)
+ {
+ if ( chrom1 > chrom2 || ((chrom1 == chrom2) && (start1 > start2)) ) {
+ swap(chrom1, chrom2);
+ swap(start1, start2);
+ swap(end1, end2);
+ swap(strand1, strand2);
+ }
+ }
+ // if -mate1First, make sure the first block is always mate 1
+ else
+ {
+ if (!bam1.IsFirstMate()) {
+ swap(chrom1, chrom2);
+ swap(start1, start2);
+ swap(end1, end2);
+ swap(strand1, strand2);
+ }
}
// report BEDPE using min mapQuality
diff --git a/src/bedToBam/Makefile b/src/bedToBam/Makefile
index e527b31..01a548a 100644
--- a/src/bedToBam/Makefile
+++ b/src/bedToBam/Makefile
@@ -8,7 +8,7 @@ BIN_DIR = ../../bin/
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp
index 6de2708..f726128 100644
--- a/src/bedToBam/bedToBam.cpp
+++ b/src/bedToBam/bedToBam.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
diff --git a/src/bedToIgv/Makefile b/src/bedToIgv/Makefile
index b6c8a68..bdd1969 100644
--- a/src/bedToIgv/Makefile
+++ b/src/bedToIgv/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/bedToIgv/bedToIgv.cpp b/src/bedToIgv/bedToIgv.cpp
index 41ace10..26b33d6 100644
--- a/src/bedToIgv/bedToIgv.cpp
+++ b/src/bedToIgv/bedToIgv.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
#include <vector>
diff --git a/src/bedpeToBam/Makefile b/src/bedpeToBam/Makefile
index 9df3c21..625234f 100644
--- a/src/bedpeToBam/Makefile
+++ b/src/bedpeToBam/Makefile
@@ -9,7 +9,7 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/bedFilePE/ \
-I$(UTILITIES_DIR)/version/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/bedpeToBam/bedpeToBam.cpp b/src/bedpeToBam/bedpeToBam.cpp
index 0e6ef2e..9a31081 100644
--- a/src/bedpeToBam/bedpeToBam.cpp
+++ b/src/bedpeToBam/bedpeToBam.cpp
@@ -11,7 +11,7 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "bedFilePE.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "version.h"
diff --git a/src/bedtools.cpp b/src/bedtools.cpp
index a0aae46..70c3e66 100644
--- a/src/bedtools.cpp
+++ b/src/bedtools.cpp
@@ -45,6 +45,7 @@ int closest_main(int argc, char* argv[]); //
int cluster_main(int argc, char* argv[]); //
int complement_main(int argc, char* argv[]);//
int coverage_main(int argc, char* argv[]); //
+int regress_test_main(int argc, char **argv); //
int expand_main(int argc, char* argv[]);//
int fastafrombed_main(int argc, char* argv[]);//
int flank_main(int argc, char* argv[]); //
@@ -59,10 +60,13 @@ int map_main(int argc, char* argv[]); //
int merge_main(int argc, char* argv[]); //
int multibamcov_main(int argc, char* argv[]);//
int multiintersect_main(int argc, char* argv[]);//
+int nek_sandbox1_main(int argc, char* argv[]);//
int nuc_main(int argc, char* argv[]);//
int pairtobed_main(int argc, char* argv[]);//
int pairtopair_main(int argc, char* argv[]);//
int random_main(int argc, char* argv[]); //
+int reldist_main(int argc, char* argv[]); //
+int sample_main(int argc, char* argv[]); //
int shuffle_main(int argc, char* argv[]); //
int slop_main(int argc, char* argv[]); //
int sort_main(int argc, char* argv[]); //
@@ -126,6 +130,7 @@ int main(int argc, char *argv[])
// statistics tools
else if (sub_cmd == "jaccard") return jaccard_main(argc-1, argv+1);
+ else if (sub_cmd == "reldist") return reldist_main(argc-1, argv+1);
// misc. tools
else if (sub_cmd == "overlap") return getoverlap_main(argc-1, argv+1);
@@ -134,9 +139,9 @@ int main(int argc, char *argv[])
else if (sub_cmd == "makewindows") return windowmaker_main(argc-1, argv+1);
else if (sub_cmd == "groupby") return groupby_main(argc-1, argv+1);
else if (sub_cmd == "expand") return expand_main(argc-1, argv+1);
-
-
-
+ else if (sub_cmd == "sample") return sample_main(argc-1, argv+1);
+ else if (sub_cmd == "neksb1") return nek_sandbox1_main(argc-1, argv+1);
+ else if (sub_cmd == "regresstest") return regress_test_main(argc, argv); //this command does need all the orig args.
// help
else if (sub_cmd == "-h" || sub_cmd == "--help" ||
sub_cmd == "-help")
@@ -198,6 +203,7 @@ int bedtools_help(void)
cout << " sort " << "Order the intervals in a file.\n";
cout << " random " << "Generate random intervals in a genome.\n";
cout << " shuffle " << "Randomly redistrubute intervals in a genome.\n";
+ cout << " sample " << "Sample random records from file using reservoir sampling.\n";
cout << " annotate " << "Annotate coverage of features from multiple files.\n";
cout << endl;
@@ -228,10 +234,11 @@ int bedtools_help(void)
cout << "[ BAM focused tools ]" << endl;
cout << " multicov " << "Counts coverage from multiple BAMs at specific intervals.\n";
cout << " tag " << "Tag BAM alignments based on overlaps with interval files.\n";
-
+
cout << endl;
- cout << "[ Statistics tools ]" << endl;
- cout << " jaccard " << "Calculates the Jaccard statistic b/w two sets of intervals.\n";
+ cout << "[ Statistical relationships ]" << endl;
+ cout << " jaccard " << "Calculate the Jaccard statistic b/w two sets of intervals.\n";
+ cout << " reldist " << "Calculate the distribution of relative distances b/w two files.\n";
cout << endl;
cout << "[ Miscellaneous tools ]" << endl;
diff --git a/src/closestBed/closestBed.cpp b/src/closestBed/closestBed.cpp
index f04e530..673028a 100644
--- a/src/closestBed/closestBed.cpp
+++ b/src/closestBed/closestBed.cpp
@@ -53,6 +53,16 @@ BedClosest::BedClosest(string &bedAFile, string &bedBFile, bool sameStrand,
BedClosest::~BedClosest(void) {
}
+void BedClosest::ReportClosestNotFound(const BED &a) {
+ _bedA->reportBedTab(a);
+ if (_reportDistance == true) {
+ _bedB->reportNullBedTab();
+ cout << -1 << endl;
+ }
+ else
+ _bedB->reportNullBedNewLine();
+}
+
void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
@@ -116,6 +126,7 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
closestB.clear();
distances.clear();
}
+ minDistance = 0;
closestB.push_back(*h);
distances.push_back(0);
}
@@ -194,58 +205,58 @@ void BedClosest::FindWindowOverlaps(BED &a, vector<BED> &hits) {
// if no overlaps were found, we'll widen the range
// by SLOPGROWTH in each direction and search again.
slop += SLOPGROWTH;
- }
- }
- // there is no feature in B on the same chromosome as A
- else {
- _bedA->reportBedTab(a);
- if (_reportDistance == true) {
- _bedB->reportNullBedTab();
- cout << -1 << endl;
- }
- else
- _bedB->reportNullBedNewLine();
- }
-
- // report the closest feature(s) in B to the current A feature.
- // obey the user's reporting request (_tieMode)
- if (numOverlaps > 0) {
- if (closestB.size() == 1 ||
- (_tieMode == "first" && closestB.size() > 0))
- {
- _bedA->reportBedTab(a);
- if (_reportDistance == true) {
- _bedB->reportBedTab(closestB[0]);
- cout << distances[0] << endl;
+ } // while ((numOverlaps == 0) && (slop <= MAXSLOP))
+
+ // report the closest feature(s) in B to the current A feature.
+ // obey the user's reporting request (_tieMode)
+ if (numOverlaps > 0) {
+ if (closestB.size() == 1 ||
+ (_tieMode == "first" && closestB.size() > 0))
+ {
+ _bedA->reportBedTab(a);
+ if (_reportDistance == true) {
+ _bedB->reportBedTab(closestB[0]);
+ cout << distances[0] << endl;
+ }
+ else
+ _bedB->reportBedNewLine(closestB[0]);
}
- else
- _bedB->reportBedNewLine(closestB[0]);
- }
- else {
- if (_tieMode == "all") {
- size_t i = 0;
- vector<BED>::iterator b = closestB.begin();
- for (; b != closestB.end(); ++b)
- {
+ else {
+ if (_tieMode == "all") {
+ size_t i = 0;
+ vector<BED>::iterator b = closestB.begin();
+ for (; b != closestB.end(); ++b)
+ {
+ _bedA->reportBedTab(a);
+ if (_reportDistance == true) {
+ _bedB->reportBedTab(*b);
+ cout << distances[i++] <<endl;
+ }
+ else
+ _bedB->reportBedNewLine(*b);
+ }
+ }
+ else if (_tieMode == "last" && closestB.size() > 0) {
_bedA->reportBedTab(a);
if (_reportDistance == true) {
- _bedB->reportBedTab(*b);
- cout << distances[i++] <<endl;
+ _bedB->reportBedTab(closestB[closestB.size()-1]);
+ cout << distances[distances.size() - 1]<<endl;
}
else
- _bedB->reportBedNewLine(*b);
- }
- }
- else if (_tieMode == "last" && closestB.size() > 0) {
- _bedA->reportBedTab(a);
- if (_reportDistance == true) {
- _bedB->reportBedTab(closestB[closestB.size()-1]);
- cout << distances[distances.size() - 1]<<endl;
+ _bedB->reportBedNewLine(closestB[closestB.size()-1]);
}
- else
- _bedB->reportBedNewLine(closestB[closestB.size()-1]);
}
}
+ // there were B features on the same chrom as A, but there were
+ // none that met the user's criteria (e.g., that it be on the
+ // same chrom)
+ else if (numOverlaps == 0) {
+ ReportClosestNotFound(a);
+ }
+ }
+ // there is no feature in B on the same chromosome as A
+ else {
+ ReportClosestNotFound(a);
}
}
diff --git a/src/closestBed/closestBed.h b/src/closestBed/closestBed.h
index dae9d56..5905186 100644
--- a/src/closestBed/closestBed.h
+++ b/src/closestBed/closestBed.h
@@ -59,8 +59,8 @@ private:
BedFile *_bedA, *_bedB;
// methods
- void reportNullB();
void FindWindowOverlaps(BED &, vector<BED> &);
+ void ReportClosestNotFound(const BED &a);
};
#endif /* CLOSEST_H */
diff --git a/src/clusterBed/clusterBed.cpp b/src/clusterBed/clusterBed.cpp
index 8790074..2bbc740 100644
--- a/src/clusterBed/clusterBed.cpp
+++ b/src/clusterBed/clusterBed.cpp
@@ -72,6 +72,8 @@ void BedCluster::ClusterBedStranded() {
// that we can easily compare "A" to it for overlaps
_bed->loadBedFileIntoMapNoBin();
+ uint32_t cluster_id = 0;
+
// loop through each chromosome and merge their BED entries
masterBedMapNoBin::const_iterator m = _bed->bedMapNoBin.begin();
masterBedMapNoBin::const_iterator mEnd = _bed->bedMapNoBin.end();
@@ -85,7 +87,6 @@ void BedCluster::ClusterBedStranded() {
vector<string> strands(2);
strands[0] = "+";
strands[1] = "-";
- uint32_t cluster_id = 0;
// do two passes, one for each strand.
for (unsigned int s = 0; s < strands.size(); s++) {
// cluster overlapping features for this chromosome.
diff --git a/src/complementBed/Makefile b/src/complementBed/Makefile
index 8b80c31..30f70b2 100644
--- a/src/complementBed/Makefile
+++ b/src/complementBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/complementBed/complementBed.h b/src/complementBed/complementBed.h
index 29a6f33..a660389 100644
--- a/src/complementBed/complementBed.h
+++ b/src/complementBed/complementBed.h
@@ -10,7 +10,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <bitset>
diff --git a/src/coverageBed/coverageMain.cpp b/src/coverageBed/coverageMain.cpp
index f13d758..05bd212 100644
--- a/src/coverageBed/coverageMain.cpp
+++ b/src/coverageBed/coverageMain.cpp
@@ -141,7 +141,7 @@ void coverage_help(void) {
cerr << "Options: " << endl;
- cerr << "\t-abam\t" << "The A input file is in BAM format." << endl << endl;
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Replaces -a." << endl << endl;
cerr << "\t-s\t" << "Require same strandedness. That is, only counts hits in A that" << endl;
cerr << "\t\toverlap B on the _same_ strand." << endl;
diff --git a/src/fastaFromBed/fastaFromBed.cpp b/src/fastaFromBed/fastaFromBed.cpp
index d9bfd05..4693994 100644
--- a/src/fastaFromBed/fastaFromBed.cpp
+++ b/src/fastaFromBed/fastaFromBed.cpp
@@ -17,14 +17,15 @@
Bed2Fa::Bed2Fa(bool useName, const string &dbFile,
const string &bedFile, const string &fastaOutFile,
bool useFasta, bool useStrand,
- bool useBlocks) :
+ bool useBlocks, bool useFullHeader) :
_useName(useName),
_dbFile(dbFile),
_bedFile(bedFile),
_fastaOutFile(fastaOutFile),
_useFasta(useFasta),
_useStrand(useStrand),
- _useBlocks(useBlocks)
+ _useBlocks(useBlocks),
+ _useFullHeader(useFullHeader)
{
_bed = new BedFile(_bedFile);
@@ -110,7 +111,7 @@ void Bed2Fa::ReportDNA(const BED &bed, string &dna) {
//******************************************************************************
void Bed2Fa::ExtractDNA() {
- /* Make sure that we can oen all of the files successfully*/
+ /* Make sure that we can open all of the files successfully*/
// open the fasta database for reading
ifstream faDb(_dbFile.c_str(), ios::in);
@@ -124,7 +125,7 @@ void Bed2Fa::ExtractDNA() {
// open and memory-map genome file
FastaReference *fr = new FastaReference;
bool memmap = true;
- fr->open(_dbFile, memmap);
+ fr->open(_dbFile, memmap, _useFullHeader);
BED bed, nullBed;
string sequence;
diff --git a/src/fastaFromBed/fastaFromBed.h b/src/fastaFromBed/fastaFromBed.h
index 76fab65..a8ff65e 100644
--- a/src/fastaFromBed/fastaFromBed.h
+++ b/src/fastaFromBed/fastaFromBed.h
@@ -33,7 +33,7 @@ public:
Bed2Fa(bool useName, const string &dbFile,
const string &bedFile, const string &fastaOutFile,
bool useFasta, bool useStrand,
- bool useBlocks);
+ bool useBlocks, bool useFullHeader);
// destructor
~Bed2Fa(void);
@@ -52,6 +52,7 @@ private:
bool _useStrand; // should the extracted sequence obey strandedness?
bool _useBlocks; // should the extracted sequence obey BED blocks
// (for example, exons?)
+ bool _useFullHeader;
// instance of a bed file class.
BedFile *_bed;
diff --git a/src/fastaFromBed/fastaFromBedMain.cpp b/src/fastaFromBed/fastaFromBedMain.cpp
index 77ba7d8..9bceb3d 100644
--- a/src/fastaFromBed/fastaFromBedMain.cpp
+++ b/src/fastaFromBed/fastaFromBedMain.cpp
@@ -44,6 +44,7 @@ int fastafrombed_main(int argc, char* argv[]) {
bool useFasta = true;
bool useStrand = false;
bool useBlocks = false;
+ bool useFullHeader = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -97,6 +98,9 @@ int fastafrombed_main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
useStrand = true;
}
+ else if(PARAMETER_CHECK("-fullHeader", 11, parameterLength)) {
+ useFullHeader = true;
+ }
else {
cerr << "*****ERROR: Unrecognized parameter: "
<< argv[i]
@@ -115,7 +119,7 @@ int fastafrombed_main(int argc, char* argv[]) {
Bed2Fa *b2f = new Bed2Fa(useNameOnly, fastaDbFile,
bedFile, fastaOutFile,
useFasta, useStrand,
- useBlocks);
+ useBlocks, useFullHeader);
delete b2f;
}
else {
@@ -148,6 +152,9 @@ void fastafrombed_help(void) {
<< endl;
cerr << "\t\tstrand, the sequence will be reverse complemented." << endl;
cerr << "\t\t- By default, strand information is ignored." << endl << endl;
+ cerr << "\t-fullHeader\tUse full fasta header." << endl;
+ cerr << "\t\t- By default, only the word before the first space or tab "
+ << "is used." << endl << endl;
// end the program here
exit(1);
diff --git a/src/flankBed/Makefile b/src/flankBed/Makefile
index e8ef3e4..ad3f0a1 100644
--- a/src/flankBed/Makefile
+++ b/src/flankBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/flankBed/flankBed.h b/src/flankBed/flankBed.h
index f344f60..995d13a 100644
--- a/src/flankBed/flankBed.h
+++ b/src/flankBed/flankBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/genomeCoverageBed/Makefile b/src/genomeCoverageBed/Makefile
index 8936fff..83e5563 100644
--- a/src/genomeCoverageBed/Makefile
+++ b/src/genomeCoverageBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/BamTools/include \
diff --git a/src/genomeCoverageBed/genomeCoverageBed.h b/src/genomeCoverageBed/genomeCoverageBed.h
index f2a877f..09df91c 100644
--- a/src/genomeCoverageBed/genomeCoverageBed.h
+++ b/src/genomeCoverageBed/genomeCoverageBed.h
@@ -10,7 +10,7 @@ aaronquinlan at gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "BlockedIntervals.h"
#include "api/BamReader.h"
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
deleted file mode 100644
index 5d115ab..0000000
--- a/src/intersectBed/intersectBed.cpp
+++ /dev/null
@@ -1,401 +0,0 @@
-/*****************************************************************************
- intersectBed.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan at gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "intersectBed.h"
-
-/************************************
-Helper functions
-************************************/
-bool BedIntersect::processHits(const BED &a, const vector<BED> &hits) {
- bool hitsFound = false;
- if (_printable == true) {
- // -wao the user wants to force the reporting of 0 overlap
- if (hits.size() == 0) {
- if (_writeAllOverlap) {
- _bedA->reportBedTab(a);
- _bedB->reportNullBedTab();
- printf("0\n");
- }
- else if (_leftJoin) {
- _bedA->reportBedTab(a);
- _bedB->reportNullBedNewLine();
- }
- }
- else {
- vector<BED>::const_iterator h = hits.begin();
- vector<BED>::const_iterator hitsEnd = hits.end();
- for (; h != hitsEnd; ++h) {
- CHRPOS s = max(a.start, h->start);
- CHRPOS e = min(a.end, h->end);
- int overlapBases = (e - s);
- ReportOverlapDetail(overlapBases, a, *h, s, e);
- hitsFound = true;
- }
- }
- }
- else {
- ReportOverlapSummary(a, hits.size());
- }
- return hitsFound;
-}
-
-
-/*
- Constructor
-*/
-BedIntersect::BedIntersect(string bedAFile, string bedBFile,
- bool anyHit, bool writeA,
- bool writeB, bool writeOverlap,
- bool writeAllOverlap, float overlapFraction,
- bool noHit, bool leftJoin,
- bool writeCount, bool sameStrand,
- bool diffStrand, bool reciprocal,
- bool obeySplits, bool bamInput,
- bool bamOutput, bool isUncompressedBam,
- bool sortedInput, bool printHeader)
-{
- _bedAFile = bedAFile;
- _bedBFile = bedBFile;
- _anyHit = anyHit;
- _noHit = noHit;
- _leftJoin = leftJoin;
- _writeA = writeA;
- _writeB = writeB;
- _writeOverlap = writeOverlap;
- _writeAllOverlap = writeAllOverlap;
- _writeCount = writeCount;
- _overlapFraction = overlapFraction;
- _sameStrand = sameStrand;
- _diffStrand = diffStrand;
- _reciprocal = reciprocal;
- _obeySplits = obeySplits;
- _bamInput = bamInput;
- _bamOutput = bamOutput;
- _isUncompressedBam = isUncompressedBam;
- _sortedInput = sortedInput;
- _printHeader = printHeader;
-
- // should we print each overlap, or does the user want summary information?
- _printable = true;
- if (_anyHit || _noHit || _writeCount)
- _printable = false;
-
- if (_bamInput == false)
- IntersectBed();
- else
- IntersectBam(bedAFile);
-}
-
-
-/*
- Destructor
-*/
-BedIntersect::~BedIntersect(void) {
-}
-
-
-bool BedIntersect::FindOverlaps(const BED &a, vector<BED> &hits) {
- bool hitsFound = false;
-
- // collect and report the sufficient hits
- _bedB->allHits(a.chrom, a.start, a.end, a.strand,
- hits, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- hitsFound = processHits(a, hits);
- return hitsFound;
-}
-
-
-bool BedIntersect::FindBlockedOverlaps(const BED &a,
- const vector<BED> &a_blocks,
- const vector<BED> &hits,
- bool a_is_bam)
-{
- int a_footprint = GetTotalBlockLength(a_blocks);
- // container to store the set of raw hits
- // that actually overlap the A blocks
- bedVector valid_hits;
- valid_hits.reserve(hits.size());
-
- // 1. Loop through each raw hit (outer loop)
- // 2. Break the raw hit into it;s blocks
- // and see of one of the hit blocks (inner loop)
- // overlaps one of a's blocks (inner, inner loop)
- // 3. If so, mark the hit as valid and add it to the valid_set.
- // Otherwise, the hit only overlapped the span of a and not
- // the individual blocks. Thus, it doesn't count.
- bedVector::const_iterator hItr = hits.begin();
- bedVector::const_iterator hEnd = hits.end();
- for (; hItr != hEnd; ++hItr) {
- // break the hit into blocks
- bedVector hitBlocks;
- GetBedBlocks(*hItr, hitBlocks);
- int b_footprint = GetTotalBlockLength(hitBlocks);
- // test to see if there is a valid hit with one of the blocks
- bool valid_hit = false;
- int total_overlap = 0;
- bedVector::const_iterator hbItr = hitBlocks.begin();
- bedVector::const_iterator hbEnd = hitBlocks.end();
- for (; hbItr != hbEnd; ++hbItr) {
- // look for overlaps between this hit/block and each block in a
- bedVector::const_iterator a_blockItr = a_blocks.begin();
- bedVector::const_iterator a_blockEnd = a_blocks.end();
- for (; a_blockItr != a_blockEnd; ++a_blockItr) {
- int hs = max(a_blockItr->start, hbItr->start);
- int he = min(a_blockItr->end, hbItr->end);
- int overlap = he - hs;
- if (overlap > 0) {
- valid_hit = true;
- total_overlap += overlap;
- }
- }
- }
- if (valid_hit) {
- // require sufficient overlap fraction (reciprocal or otherwise)
- // w.r.t to the "footprint" (i.e., the total length of each block)
- if ( ((float) total_overlap
- /
- (float) a_footprint) > _overlapFraction)
- {
- if (_reciprocal && ((float) total_overlap /
- (float) b_footprint) > _overlapFraction)
- {
- valid_hits.push_back(*hItr);
- }
- else if (!_reciprocal) {
- valid_hits.push_back(*hItr);
- }
- }
- }
- }
- if (!a_is_bam) {
- return processHits(a, valid_hits);
- }
- else
- return !valid_hits.empty();
-}
-
-
-void BedIntersect::ReportOverlapDetail(int overlapBases, const BED &a,
- const BED &b, CHRPOS s, CHRPOS e)
-{
- // default. simple intersection only
- if (_writeA == false && _writeB == false &&
- _writeOverlap == false && _leftJoin == false)
- {
- _bedA->reportBedRangeNewLine(a,s,e);
- }
- // -wa -wb write the original A and B
- else if ((_writeA == true && _writeB == true) || _leftJoin == true) {
- _bedA->reportBedTab(a);
- _bedB->reportBedNewLine(b);
- }
- // -wa write just the original A
- else if (_writeA == true) {
- _bedA->reportBedNewLine(a);
- }
- // -wb write the intersected portion of A and the original B
- else if (_writeB == true) {
- _bedA->reportBedRangeTab(a,s,e);
- _bedB->reportBedNewLine(b);
- }
- // -wo write the original A and B plus the no. of overlapping bases.
- else if (_writeOverlap == true) {
- _bedA->reportBedTab(a);
- _bedB->reportBedTab(b);
- if (b.zeroLength == false) printf("%d\n", overlapBases);
- else printf("0\n");
- }
-}
-
-
-void BedIntersect::ReportOverlapSummary(const BED &a, const int &numOverlapsFound) {
- // -u just report the fact that there was >= 1 overlaps
- if (_anyHit && (numOverlapsFound >= 1)) {
- _bedA->reportBedNewLine(a);
- }
- // -c report the total number of features overlapped in B
- else if (_writeCount) {
- _bedA->reportBedTab(a);
- printf("%d\n", numOverlapsFound);
- }
- // -v report iff there were no overlaps
- else if (_noHit && (numOverlapsFound == 0)) {
- _bedA->reportBedNewLine(a);
- }
-}
-
-
-void BedIntersect::IntersectBed() {
-
- // create new BED file objects for A and B
- _bedA = new BedFile(_bedAFile);
- _bedB = new BedFile(_bedBFile);
-
- if (_sortedInput == false) {
- // load the "B" file into a map in order to
- // compare each entry in A to it in search of overlaps.
- _bedB->loadBedFileIntoMap();
-
- vector<BED> hits;
- hits.reserve(100);
- BED a;
-
- // open the "A" file, process each BED entry and searh for overlaps.
- _bedA->Open();
- // report A's header first if asked.
- if (_printHeader == true) {
- _bedA->PrintHeader();
- }
- while (_bedA->GetNextBed(a)) {
- if (_bedA->_status == BED_VALID) {
- // treat the BED as a single "block"
- if (_obeySplits == false)
- FindOverlaps(a, hits);
- // split the BED12 into blocks and look for
- // overlaps in each discrete block
- else {
- // find the hits that overlap with the
- // full span of the blocked BED
- _bedB->allHits(a.chrom, a.start, a.end, a.strand,
- hits, _sameStrand, _diffStrand,
- 0.0, false);
- // break a into discrete blocks, as we need to
- // measure overlap with the individual blocks,
- // not the full span.
- bedVector a_blocks;
- GetBedBlocks(a, a_blocks);
- // find the overlaps between the block in A and B
- // last parm is false as a is not a BAM entry
- FindBlockedOverlaps(a, a_blocks, hits, false);
- }
- hits.clear();
- }
- }
- _bedA->Close();
- }
- else {
- // use the chromsweep algorithm to detect overlaps on the fly.
- ChromSweep sweep = ChromSweep(_bedA, _bedB,
- _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal,
- false, _printHeader);
-
- pair<BED, vector<BED> > hit_set;
- hit_set.second.reserve(10000);
- while (sweep.Next(hit_set)) {
- if (_obeySplits == false) {
- processHits(hit_set.first, hit_set.second);
- }
- else {
- bedVector a_blocks;
- GetBedBlocks(hit_set.first, a_blocks);
- FindBlockedOverlaps(hit_set.first, a_blocks,
- hit_set.second, false);
- }
- }
- }
-}
-
-
-void BedIntersect::IntersectBam(string bamFile) {
-
- // load the "B" bed file into a map so
- // that we can easily compare "A" to it for overlaps
- _bedB = new BedFile(_bedBFile);
- _bedB->loadBedFileIntoMap();
-
- // create a dummy BED A file for printing purposes if not
- // using BAM output.
- if (_bamOutput == false) {
- _bedA = new BedFile(_bedAFile);
- _bedA->bedType = 12;
- }
- // open the BAM file
- BamReader reader;
- BamWriter writer;
- if (!reader.Open(bamFile)) {
- cerr << "Failed to open BAM file " << bamFile << endl;
- exit(1);
- }
-
- // get header & reference information
- string bamHeader = reader.GetHeaderText();
- RefVector refs = reader.GetReferenceData();
- // open a BAM output to stdout if we are writing BAM
- if (_bamOutput == true) {
- // set compression mode
- BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
- if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
- writer.SetCompressionMode(compressionMode);
- // open our BAM writer
- writer.Open("stdout", bamHeader, refs);
- }
- vector<BED> hits;
- // reserve some space
- hits.reserve(100);
- BamAlignment bam;
- // get each set of alignments for each pair.
- while (reader.GetNextAlignment(bam)) {
-
- // save an unaligned read if -v
- if (!bam.IsMapped()) {
- if ((_noHit == true) && (_bamOutput == true))
- writer.SaveAlignment(bam);
- continue;
- }
- // break alignment into discrete blocks,
- bedVector bed_blocks;
- string chrom = refs.at(bam.RefID).RefName;
- GetBamBlocks(bam, chrom, bed_blocks, false, true);
- // create a basic BED entry from the BAM alignment
- BED bed;
- MakeBedFromBam(bam, chrom, bed_blocks, bed);
- bool overlapsFound = false;
- if ((_bamOutput == true) && (_obeySplits == false))
- {
- overlapsFound = _bedB->anyHits(bed.chrom, bed.start, bed.end,
- bed.strand, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- }
- else if ( ((_bamOutput == true) && (_obeySplits == true)) ||
- ((_bamOutput == false) && (_obeySplits == true)) )
- {
- // find the hits that overlap with the full span of the blocked BED
- _bedB->allHits(bed.chrom, bed.start, bed.end, bed.strand,
- hits, _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal);
- // find the overlaps between the block in A and B
- overlapsFound =
- FindBlockedOverlaps(bed, bed_blocks, hits, _bamOutput);
- }
- else if ((_bamOutput == false) && (_obeySplits == false))
- {
- FindOverlaps(bed, hits);
- }
- // save the BAM alignment if overlap reqs. were met
- if (_bamOutput == true) {
- if ((overlapsFound == true) && (_noHit == false))
- writer.SaveAlignment(bam);
- else if ((overlapsFound == false) && (_noHit == true))
- writer.SaveAlignment(bam);
- }
- hits.clear();
- }
-
- // close the relevant BAM files.
- reader.Close();
- if (_bamOutput == true) {
- writer.Close();
- }
-}
-
diff --git a/src/intersectBed/intersectBed.h b/src/intersectBed/intersectBed.h
deleted file mode 100644
index 5a10a81..0000000
--- a/src/intersectBed/intersectBed.h
+++ /dev/null
@@ -1,102 +0,0 @@
-/*****************************************************************************
- intersectBed.h
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan at gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef INTERSECTBED_H
-#define INTERSECTBED_H
-
-#include "bedFile.h"
-#include "chromsweep.h"
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-#include "BlockedIntervals.h"
-#include "BamAncillary.h"
-using namespace BamTools;
-
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
-using namespace std;
-
-
-
-class BedIntersect {
-
-public:
-
- // constructor
- BedIntersect(string bedAFile, string bedBFile, bool anyHit,
- bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
- float overlapFraction, bool noHit, bool leftJoin, bool writeCount, bool sameStrand, bool diffStrand,
- bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput, bool isUncompressedBam,
- bool sortedInput, bool printHeader);
-
- // destructor
- ~BedIntersect(void);
-
-private:
-
- //------------------------------------------------
- // private attributes
- //------------------------------------------------
- string _bedAFile;
- string _bedBFile;
-
- bool _writeA; // should the original A feature be reported?
- bool _writeB; // should the original B feature be reported?
- bool _writeOverlap;
- bool _writeAllOverlap;
-
- bool _sameStrand;
- bool _diffStrand;
- bool _reciprocal;
- float _overlapFraction;
-
- bool _anyHit;
- bool _noHit;
- bool _leftJoin;
- bool _writeCount; // do we want a count of the number of overlaps in B?
- bool _obeySplits;
- bool _bamInput;
- bool _bamOutput;
- bool _isUncompressedBam;
- bool _sortedInput;
- bool _printable;
- bool _printHeader;
-
- // instance of a bed file class.
- BedFile *_bedA, *_bedB;
-
- //------------------------------------------------
- // private methods
- //------------------------------------------------
- void IntersectBed(istream &bedInput);
-
- void IntersectBed();
-
- void IntersectBam(string bamFile);
-
- bool processHits(const BED &a, const vector<BED> &hits);
-
- bool FindOverlaps(const BED &a, vector<BED> &hits);
-
- bool FindBlockedOverlaps(const BED &a, const vector<BED> &a_blocks,
- const vector<BED> &hits, bool a_is_bam);
-
- void ReportOverlapDetail(int overlapBases, const BED &a, const BED &b, CHRPOS s, CHRPOS e);
-
- void ReportOverlapSummary(const BED &a, const int &numOverlapsFound);
-
-};
-
-#endif /* INTERSECTBED_H */
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
deleted file mode 100644
index f1d26a2..0000000
--- a/src/intersectBed/intersectMain.cpp
+++ /dev/null
@@ -1,326 +0,0 @@
-/*****************************************************************************
- intersectMain.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan at gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "intersectBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "bedtools intersect"
-
-
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
-
-// function declarations
-void intersect_help(void);
-
-int intersect_main(int argc, char* argv[]) {
-
- // our configuration variables
- bool showHelp = false;
-
- // input files
- string bedAFile;
- string bedBFile;
-
- // input arguments
- float overlapFraction = 1E-9;
-
- bool haveBedA = false;
- bool haveBedB = false;
- bool noHit = false;
- bool leftJoin = false;
- bool anyHit = false;
- bool writeA = false;
- bool writeB = false;
- bool writeCount = false;
- bool writeOverlap = false;
- bool writeAllOverlap = false;
- bool haveFraction = false;
- bool reciprocalFraction = false;
- bool sameStrand = false;
- bool diffStrand = false;
- bool obeySplits = false;
- bool inputIsBam = false;
- bool outputIsBam = true;
- bool uncompressedBam = false;
- bool sortedInput = false;
- bool printHeader = false;
-
- // check to see if we should print out some help
- if(argc <= 1) showHelp = true;
-
- for(int i = 1; i < argc; i++) {
- int parameterLength = (int)strlen(argv[i]);
-
- if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
- (PARAMETER_CHECK("--help", 5, parameterLength))) {
- showHelp = true;
- }
- }
-
- if(showHelp) intersect_help();
-
- // do some parsing (all of these parameters require 2 strings)
- for(int i = 1; i < argc; i++) {
-
- int parameterLength = (int)strlen(argv[i]);
-
- if(PARAMETER_CHECK("-a", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveBedA = true;
- outputIsBam = false;
- bedAFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
- if ((i+1) < argc) {
- haveBedA = true;
- inputIsBam = true;
- bedAFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveBedB = true;
- bedBFile = argv[i + 1];
- i++;
- }
- }
- else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
- outputIsBam = false;
- }
- else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
- anyHit = true;
- }
- else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveFraction = true;
- overlapFraction = atof(argv[i + 1]);
- i++;
- }
- }
- else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
- writeA = true;
- }
- else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
- writeB = true;
- }
- else if(PARAMETER_CHECK("-wo", 3, parameterLength)) {
- writeOverlap = true;
- }
- else if(PARAMETER_CHECK("-wao", 4, parameterLength)) {
- writeAllOverlap = true;
- writeOverlap = true;
- }
- else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
- writeCount = true;
- }
- else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
- reciprocalFraction = true;
- }
- else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
- noHit = true;
- }
- else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
- sameStrand = true;
- }
- else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
- diffStrand = true;
- }
- else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
- obeySplits = true;
- }
- else if (PARAMETER_CHECK("-loj", 4, parameterLength)) {
- leftJoin = true;
- }
- else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
- uncompressedBam = true;
- }
- else if(PARAMETER_CHECK("-sorted", 7, parameterLength)) {
- sortedInput = true;
- }
- else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
- printHeader = true;
- }
- else {
- cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
- showHelp = true;
- }
- }
-
- // make sure we have both input files
- if (!haveBedA || !haveBedB) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && noHit) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeB && writeCount) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeCount && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeA && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (writeB && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (reciprocalFraction && !haveFraction) {
- cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeCount) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeB) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (anyHit && writeOverlap) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (sameStrand && diffStrand) {
- cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
- showHelp = true;
- }
-
- if (inputIsBam && writeB && outputIsBam) {
- cerr << endl << "*****" << endl << "*****WARNING: -wb is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (inputIsBam && leftJoin) {
- cerr << endl << "*****" << endl << "*****WARNING: -loj is ignored with -abam" << endl << "*****" << endl;
- }
-
- if (outputIsBam && (writeCount || writeOverlap || writeAllOverlap))
- {
- outputIsBam = false;
- }
-
- if (!showHelp) {
-
- BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap,
- writeAllOverlap, overlapFraction, noHit, leftJoin, writeCount, sameStrand, diffStrand,
- reciprocalFraction, obeySplits, inputIsBam, outputIsBam, uncompressedBam,
- sortedInput, printHeader);
- delete bi;
- return 0;
- }
- else {
- intersect_help();
- return 0;
- }
-}
-
-void intersect_help(void) {
-
- cerr << "\nTool: bedtools intersect (aka intersectBed)" << endl;
- cerr << "Version: " << VERSION << "\n";
- cerr << "Summary: Report overlaps between two feature files." << endl << endl;
-
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
-
- cerr << "Options: " << endl;
-
- cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
-
- cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
-
- cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
- cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
-
- cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
-
- cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
- cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
-
- cerr << "\t-loj\t" << "Perform a \"left outer join\". That is, for each feature in A" << endl;
- cerr << "\t\treport each overlap with B. If no overlaps are found, " << endl;
- cerr << "\t\treport a NULL feature for B." << endl << endl;
-
- cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
- cerr << "\t\tpairs of overlap between the two features." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
- cerr << "\t\t Only A features with overlap are reported." << endl << endl;
-
- cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
- cerr << "\t\tpairs of overlap between the two features." << endl;
- cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
- cerr << "\t\t However, A features w/o overlap are also reported" << endl;
- cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
-
- cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
- cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
-
- cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
- cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
- cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
-
- cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
- cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
-
- cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
- cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
- cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
-
- cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
- cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
- cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
-
- cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B" << endl;
- cerr << "\t\tthat overlap A on the _same_ strand." << endl;
- cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
-
- cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B" << endl;
- cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
- cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
-
- cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
-
- cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl << endl;
-
- cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
-
- cerr << "Notes: " << endl;
- cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
- cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
- cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl;
-
- // end the program here
- exit(1);
-
-}
diff --git a/src/intersectFile/Makefile b/src/intersectFile/Makefile
new file mode 100644
index 0000000..e265b33
--- /dev/null
+++ b/src/intersectFile/Makefile
@@ -0,0 +1,45 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src \
+ -I$(UTILITIES_DIR)/BlockedIntervals \
+ -I$(UTILITIES_DIR)/BamTools-Ancillary \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+ -I$(UTILITIES_DIR)/NewChromsweep \
+ -I$(UTILITIES_DIR)/BinTree \
+ -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= intersectMain.cpp intersectFile.cpp intersectFile.h
+OBJECTS= intersectMain.o intersectFile.o
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= intersectFile
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectFile.o
+
+.PHONY: clean
diff --git a/src/intersectFile/intersectFile.cpp b/src/intersectFile/intersectFile.cpp
new file mode 100644
index 0000000..928d1d9
--- /dev/null
+++ b/src/intersectFile/intersectFile.cpp
@@ -0,0 +1,105 @@
+/*****************************************************************************
+ intersectFile.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+
+#include "intersectFile.h"
+#include "ContextIntersect.h"
+#include "FileRecordMgr.h"
+#include "NewChromsweep.h"
+#include "BinTree.h"
+#include "RecordOutputMgr.h"
+
+
+FileIntersect::FileIntersect(ContextIntersect *context)
+: _context(context),
+ _blockMgr(NULL),
+ _recordOutputMgr(NULL)
+{
+ _recordOutputMgr = new RecordOutputMgr();
+ _recordOutputMgr->init(_context);
+ if (_context->getObeySplits()) {
+ _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
+ _recordOutputMgr->setSplitInfo(_blockMgr);
+ }
+}
+
+FileIntersect::~FileIntersect(void) {
+ delete _blockMgr;
+ _blockMgr = NULL;
+ delete _recordOutputMgr;
+}
+
+void FileIntersect::processHits(RecordKeyList &hits) {
+ _recordOutputMgr->printRecord(hits);
+}
+
+bool FileIntersect::intersectFiles()
+{
+ if (_context->getSortedInput()) {
+ return processSortedFiles();
+ }
+ return processUnsortedFiles();
+}
+
+bool FileIntersect::processSortedFiles()
+{
+ // use the chromsweep algorithm to detect overlaps on the fly.
+ NewChromSweep sweep(_context);
+
+ if (!sweep.init()) {
+ return false;
+ }
+
+ RecordKeyList hitSet;
+ while (sweep.next(hitSet)) {
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet(hitSet.getKey());
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ processHits(resultSet);
+ } else {
+ processHits(hitSet);
+ }
+ }
+ return true;
+}
+
+bool FileIntersect::processUnsortedFiles()
+{
+ BinTree *binTree = new BinTree( _context);
+ binTree->loadDB();
+
+ FileRecordMgr *queryFRM = _context->getFile(_context->getQueryFileIdx());
+
+
+ while (!queryFRM->eof()) {
+ Record *queryRecord = queryFRM->allocateAndGetNextRecord();
+ if (queryRecord == NULL) {
+ continue;
+ }
+ RecordKeyList hitSet(queryRecord);
+ binTree->getHits(queryRecord, hitSet);
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet;
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ processHits(resultSet);
+ } else {
+ processHits(hitSet);
+ }
+ queryFRM->deleteRecord(queryRecord);
+ }
+ queryFRM->close();
+
+ //clean up.
+ delete binTree;
+ return true;
+}
diff --git a/src/intersectFile/intersectFile.h b/src/intersectFile/intersectFile.h
new file mode 100644
index 0000000..c1f8674
--- /dev/null
+++ b/src/intersectFile/intersectFile.h
@@ -0,0 +1,46 @@
+/*****************************************************************************
+ intersectFile.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#ifndef INTERSECTFILE_H
+#define INTERSECTFILE_H
+
+using namespace std;
+
+#include "RecordKeyList.h"
+
+using namespace std;
+
+class ContextIntersect;
+class BlockMgr;
+class RecordOutputMgr;
+
+class FileIntersect {
+
+public:
+ FileIntersect(ContextIntersect *context);
+ ~FileIntersect(void);
+
+ bool intersectFiles();
+
+private:
+ ContextIntersect *_context;
+ Record *_queryRec;
+ Record *_databaseRec;
+ BlockMgr *_blockMgr;
+ RecordOutputMgr *_recordOutputMgr;
+
+ void processHits(RecordKeyList &hits);
+ bool processSortedFiles();
+ bool processUnsortedFiles();
+
+};
+
+#endif /* INTERSECTFILE_H */
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
new file mode 100644
index 0000000..9f38f3c
--- /dev/null
+++ b/src/intersectFile/intersectMain.cpp
@@ -0,0 +1,130 @@
+/*****************************************************************************
+ intersectMain.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+using namespace std;
+
+#include "intersectFile.h"
+#include "ContextIntersect.h"
+
+// define our program name
+#define PROGRAM_NAME "bedtools intersect"
+
+void intersect_help(void);
+
+int intersect_main(int argc, char* argv[]) {
+
+ ContextIntersect *context = new ContextIntersect();
+ if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+ if (!context->getErrorMsg().empty()) {
+ cerr << context->getErrorMsg() << endl;
+ }
+ intersect_help();
+ delete context;
+ return 0;
+ }
+ FileIntersect *fileIntersect = new FileIntersect(context);
+
+ bool retVal = fileIntersect->intersectFiles();
+ delete fileIntersect;
+ delete context;
+ return retVal ? 0 : 1;
+}
+
+void intersect_help(void) {
+
+ cerr << "\nTool: bedtools intersect (aka intersectBed)" << endl;
+ cerr << "Version: " << VERSION << "\n";
+ cerr << "Summary: Report overlaps between two feature files." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
+
+ cerr << "Options: " << endl;
+
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
+
+ cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
+
+ cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
+ cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
+
+ cerr << "\t-wa\t" << "Write the original entry in A for each overlap." << endl << endl;
+
+ cerr << "\t-wb\t" << "Write the original entry in B for each overlap." << endl;
+ cerr << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-loj\t" << "Perform a \"left outer join\". That is, for each feature in A" << endl;
+ cerr << "\t\treport each overlap with B. If no overlaps are found, " << endl;
+ cerr << "\t\treport a NULL feature for B." << endl << endl;
+
+ cerr << "\t-wo\t" << "Write the original A and B entries plus the number of base" << endl;
+ cerr << "\t\tpairs of overlap between the two features." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl;
+ cerr << "\t\t Only A features with overlap are reported." << endl << endl;
+
+ cerr << "\t-wao\t" << "Write the original A and B entries plus the number of base" << endl;
+ cerr << "\t\tpairs of overlap between the two features." << endl;
+ cerr << "\t\t- Overlapping features restricted by -f and -r." << endl;
+ cerr << "\t\t However, A features w/o overlap are also reported" << endl;
+ cerr << "\t\t with a NULL B feature and overlap = 0." << endl << endl;
+
+ cerr << "\t-u\t" << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
+ cerr << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-c\t" << "For each entry in A, report the number of overlaps with B." << endl;
+ cerr << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
+ cerr << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+ cerr << "\t-v\t" << "Only report those entries in A that have _no overlaps_ with B." << endl;
+ cerr << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
+
+ cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
+ cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
+ cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+
+ cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
+ cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
+ cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
+
+ cerr << "\t-s\t" << "Require same strandedness. That is, only report hits in B" << endl;
+ cerr << "\t\tthat overlap A on the _same_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in B" << endl;
+ cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
+ cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
+ cerr << "\t-sorted\t" << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input." << endl << endl;
+
+ cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
+ cerr <<"\t\tacross input files. Only applies when used with -sorted option." << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the A file prior to results." << endl << endl;
+
+ cerr << "\t-nobuf\t" << "Disable buffered output. Using this option will cause each line"<< endl;
+ cerr <<"\t\tof output to be printed as it is generated, rather than saved" << endl;
+ cerr <<"\t\tin a buffer. This will make printing large output files " << endl;
+
+ cerr <<"\t\tnoticeably slower, but can be useful in conjunction with" << endl;
+ cerr <<"\t\tother software tools and scripts that need to process one" << endl;
+ cerr <<"\t\tline of bedtools output at a time." << endl << endl;
+
+ cerr << "Notes: " << endl;
+ cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
+ cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
+ cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl;
+
+ // end the program here
+ exit(1);
+
+}
diff --git a/src/jaccard/jaccard.cpp b/src/jaccard/jaccard.cpp
index 99929fa..147ee4e 100644
--- a/src/jaccard/jaccard.cpp
+++ b/src/jaccard/jaccard.cpp
@@ -34,12 +34,14 @@ size_t Jaccard::GetTotalIntersection(const BED &a, const vector<BED> &hits)
Constructor
*/
Jaccard::Jaccard(string bedAFile, string bedBFile,
- float overlapFraction, bool reciprocal)
+ float overlapFraction, bool reciprocal,
+ bool valueOnly)
{
_bedAFile = bedAFile;
_bedBFile = bedBFile;
_overlapFraction = overlapFraction;
_reciprocal = reciprocal;
+ _valueOnly = valueOnly;
CalculateJaccard();
@@ -53,28 +55,7 @@ Jaccard::~Jaccard(void) {
}
-unsigned long Jaccard::GetUnion() {
-
- // create new BED file objects for A and B
- _bedA = new BedFile(_bedAFile);
- _bedB = new BedFile(_bedBFile);
-
- unsigned long U = 0;
- BED bed;
- _bedA->Open();
- while (_bedA->GetNextMergedBed(bed)) {
- U += bed.end - bed.start;
- }
-
- _bedB->Open();
- while (_bedB->GetNextMergedBed(bed)) {
- U += bed.end - bed.start;
- }
-
- return U;
-}
-
-unsigned long Jaccard::GetIntersection() {
+unsigned long Jaccard::GetIntersection(size_t &n_intersections) {
_bedA = new BedFile(_bedAFile);
_bedB = new BedFile(_bedBFile);
@@ -91,28 +72,39 @@ unsigned long Jaccard::GetIntersection() {
hit_set.second.reserve(10000);
while (sweep.Next(hit_set)) {
I += GetTotalIntersection(hit_set.first, hit_set.second);
+ n_intersections += hit_set.second.size();
}
return I;
}
void Jaccard::CalculateJaccard() {
- unsigned long U = GetUnion();
- delete _bedA;
- delete _bedB;
- unsigned long I = GetIntersection();
+ size_t n_intersections = 0;
+ unsigned long I = GetIntersection(n_intersections);
- // header
- cout << "intersection\t"
- << "union\t"
- << "jaccard"
- << endl;
+ unsigned long U = _bedA->getTotalFlattenedLength() + \
+ _bedB->getTotalFlattenedLength();
- // result
- cout << I << "\t"
- << U - I << "\t"
- << (float) I / ((float) U - (float) I)
- << endl;
+ float jaccard_stat = (float) I / ((float) U - (float) I);
+
+ if (!_valueOnly) {
+ // header
+ cout << "intersection\t"
+ << "union-intersection\t"
+ << "jaccard\t"
+ << "n_intersections"
+ << endl;
+
+ // result
+ cout << I << "\t"
+ << U - I << "\t"
+ << jaccard_stat << "\t"
+ << n_intersections
+ << endl;
+ }
+ else {
+ cout << jaccard_stat << endl;
+ }
}
diff --git a/src/jaccard/jaccard.h b/src/jaccard/jaccard.h
index f0e3fd7..2badb00 100644
--- a/src/jaccard/jaccard.h
+++ b/src/jaccard/jaccard.h
@@ -35,7 +35,8 @@ public:
// constructor
Jaccard(string bedAFile, string bedBFile,
- float overlapFraction, bool reciprocal);
+ float overlapFraction, bool reciprocal,
+ bool valueOnly);
// destructor
~Jaccard(void);
@@ -49,6 +50,7 @@ private:
string _bedBFile;
bool _reciprocal;
+ bool _valueOnly;
float _overlapFraction;
// instance of a bed file class.
@@ -57,7 +59,7 @@ private:
//------------------------------------------------
// private methods
//------------------------------------------------
- unsigned long GetIntersection();
+ unsigned long GetIntersection(size_t &n_intersections);
unsigned long GetUnion();
void CalculateJaccard();
diff --git a/src/jaccard/jaccardMain.cpp b/src/jaccard/jaccardMain.cpp
index cc175d1..683306d 100644
--- a/src/jaccard/jaccardMain.cpp
+++ b/src/jaccard/jaccardMain.cpp
@@ -40,6 +40,7 @@ int jaccard_main(int argc, char* argv[]) {
bool haveBedB = false;
bool haveFraction = false;
bool reciprocalFraction = false;
+ bool valueOnly = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -84,6 +85,9 @@ int jaccard_main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
reciprocalFraction = true;
}
+ else if(PARAMETER_CHECK("-valueOnly", 10, parameterLength)) {
+ valueOnly = true;
+ }
else {
cerr << endl
<< "*****ERROR: Unrecognized parameter: "
@@ -108,7 +112,8 @@ int jaccard_main(int argc, char* argv[]) {
if (!showHelp) {
Jaccard *j = new Jaccard(bedAFile, bedBFile,
- overlapFraction, reciprocalFraction);
+ overlapFraction, reciprocalFraction,
+ valueOnly);
delete j;
return 0;
}
diff --git a/src/mapBed/mapBed.cpp b/src/mapBed/mapBed.cpp
deleted file mode 100644
index c7faf4b..0000000
--- a/src/mapBed/mapBed.cpp
+++ /dev/null
@@ -1,122 +0,0 @@
-/*****************************************************************************
- mapBed.cpp
-
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan at gmail.com
-
- Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "mapBed.h"
-
-const int PRECISION = 21;
-double GetUserColumn(const string s);
-
-// Constructor
-BedMap::BedMap(string bedAFile, string bedBFile, int column, string operation,
- float overlapFraction, bool sameStrand,
- bool diffStrand, bool reciprocal,
- bool choseNullValue, string nullValue,
- bool printHeader)
-{
-
- _bedAFile = bedAFile;
- _bedBFile = bedBFile;
- _column = column - 1; // user's request is 1-based
- _operation = operation;
- _overlapFraction = overlapFraction;
- _sameStrand = sameStrand;
- _diffStrand = diffStrand;
- _reciprocal = reciprocal;
- _nullValue = nullValue;
- _printHeader = printHeader;
-
- if (!choseNullValue && operation == "count")
- _nullValue = "0";
- Map();
-}
-
-// Destructor
-BedMap::~BedMap(void)
-{}
-
-void BedMap::Map() {
-
- // create new BED file objects for A and B
- _bedA = new BedFile(_bedAFile);
- _bedB = new BedFile(_bedBFile);
-
- // use the chromsweep algorithm to detect overlaps on the fly.
- ChromSweep sweep = ChromSweep(_bedA, _bedB,
- _sameStrand, _diffStrand,
- _overlapFraction, _reciprocal,
- false, _printHeader);
-
- pair<BED, vector<BED> > hit_set;
- hit_set.second.reserve(10000);
- while (sweep.Next(hit_set)) {
- string result = MapHits(hit_set.first, hit_set.second);
- _bedA->reportBedTab(hit_set.first);
- printf("%s\n", result.c_str());
- }
-}
-
-
-string BedMap::MapHits(const BED &a, const vector<BED> &hits) {
-
- ostringstream output;
- if (hits.size() == 0)
- return _nullValue;
-
- ExtractColumnFromHits(hits);
- VectorOps vo(_column_vec);
- if (_operation == "sum")
- output << setprecision (PRECISION) << vo.GetSum();
- else if (_operation == "mean")
- output << setprecision (PRECISION) << vo.GetMean();
- else if (_operation == "median")
- output << setprecision (PRECISION) << vo.GetMedian();
- else if (_operation == "min")
- output << setprecision (PRECISION) << vo.GetMin();
- else if (_operation == "max")
- output << setprecision (PRECISION) << vo.GetMax();
- else if (_operation == "mode")
- output << vo.GetMode();
- else if (_operation == "antimode")
- output << vo.GetAntiMode();
- else if (_operation == "count")
- output << setprecision (PRECISION) << vo.GetCount();
- else if (_operation == "count_distinct")
- output << setprecision (PRECISION) << vo.GetCountDistinct();
- else if (_operation == "collapse")
- output << vo.GetCollapse();
- else if (_operation == "distinct")
- output << vo.GetDistinct();
- else {
- cerr << "ERROR: " << _operation << " is an unrecoginzed operation\n";
- exit(1);
- }
- _column_vec.clear();
- return output.str();
-}
-
-
-void BedMap::ExtractColumnFromHits(const vector<BED> &hits) {
- for (size_t i = 0; i < hits.size(); ++i) {
- try {
- _column_vec.push_back(hits[i].fields.at(_column));
- }
- catch(std::out_of_range& e) {
- cerr << endl << "*****" << endl
- << "*****ERROR: requested column ("
- << _column + 1
- << ") exceeds the number of columns in file at line "
- << _bedA->_lineNum << ". Exiting."
- << endl << "*****" << endl;
- exit(1);
- }
- }
-}
diff --git a/src/mapFile/Makefile b/src/mapFile/Makefile
new file mode 100644
index 0000000..17bb42d
--- /dev/null
+++ b/src/mapFile/Makefile
@@ -0,0 +1,56 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+# INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+# -I$(UTILITIES_DIR)/gzstream/ \
+# -I$(UTILITIES_DIR)/genomeFile/ \
+# -I$(UTILITIES_DIR)/lineFileUtilities/ \
+# -I$(UTILITIES_DIR)/fileType/ \
+# -I$(UTILITIES_DIR)/BamTools/include \
+# -I$(UTILITIES_DIR)/BamTools-Ancillary \
+# -I$(UTILITIES_DIR)/chromsweep \
+# -I$(UTILITIES_DIR)/VectorOps \
+# -I$(UTILITIES_DIR)/version/
+
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src \
+ -I$(UTILITIES_DIR)/BlockedIntervals \
+ -I$(UTILITIES_DIR)/BamTools-Ancillary \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+ -I$(UTILITIES_DIR)/NewChromsweep \
+ -I$(UTILITIES_DIR)/VectorOps \
+ -I$(UTILITIES_DIR)/BinTree \
+ -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= mapMain.cpp mapFile.cpp mapFile.h
+OBJECTS= mapMain.o mapFile.o
+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) $(DFLAGS) $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/mapMain.o $(OBJ_DIR)/mapFile.o
+
+.PHONY: clean
diff --git a/src/mapFile/mapFile.cpp b/src/mapFile/mapFile.cpp
new file mode 100644
index 0000000..88dcc26
--- /dev/null
+++ b/src/mapFile/mapFile.cpp
@@ -0,0 +1,120 @@
+/*****************************************************************************
+ mapBed.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "mapFile.h"
+#include "ContextMap.h"
+#include "FileRecordMgr.h"
+#include "NewChromsweep.h"
+#include "BinTree.h"
+#include "RecordOutputMgr.h"
+
+const int PRECISION = 21;
+
+FileMap::FileMap(ContextMap *context)
+: _context(context),
+ _blockMgr(NULL),
+ _recordOutputMgr(NULL)
+{
+ _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
+ _recordOutputMgr = new RecordOutputMgr();
+ _recordOutputMgr->init(_context);
+}
+
+FileMap::~FileMap(void) {
+ delete _blockMgr;
+ _blockMgr = NULL;
+ delete _recordOutputMgr;
+ _recordOutputMgr = NULL;
+}
+
+bool FileMap::mapFiles()
+{
+ NewChromSweep sweep(_context);
+ if (!sweep.init()) {
+ return false;
+ }
+ RecordKeyList hitSet;
+ while (sweep.next(hitSet)) {
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet(hitSet.getKey());
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ SummarizeHits(resultSet);
+ _recordOutputMgr->printRecord(resultSet.getKey(), _output);
+ } else {
+ SummarizeHits(hitSet);
+ _recordOutputMgr->printRecord(hitSet.getKey(), _output);
+ }
+ }
+ return true;
+}
+
+void FileMap::ExtractColumnFromHits(RecordKeyList &hits) {
+ _column_vec.clear();
+ RecordKeyList::const_iterator_type iter = hits.begin();
+ for (; iter != hits.end(); iter = hits.next())
+ {
+ _column_vec.push_back(iter->value()->getField(_context->getColumn()).str());
+ }
+}
+
+void FileMap::SummarizeHits(RecordKeyList &hits) {
+
+ const QuickString & operation = _context->getColumnOperation();
+ _output.clear();
+
+ if (hits.size() == 0) {
+ if (operation == "count" || operation == "count_distinct")
+ _output.append("0");
+ else
+ _output.append(_context->getNullValue().str());
+ return;
+ }
+
+ _tmp_output.str("");
+ _tmp_output.clear();
+
+ ExtractColumnFromHits(hits);
+
+ VectorOps vo(_column_vec);
+ if (operation == "sum")
+ _tmp_output << setprecision (PRECISION) << vo.GetSum();
+ else if (operation == "mean")
+ _tmp_output << setprecision (PRECISION) << vo.GetMean();
+ else if (operation == "median")
+ _tmp_output << setprecision (PRECISION) << vo.GetMedian();
+ else if (operation == "min")
+ _tmp_output << setprecision (PRECISION) << vo.GetMin();
+ else if (operation == "max")
+ _tmp_output << setprecision (PRECISION) << vo.GetMax();
+ else if (operation == "absmin")
+ _tmp_output << setprecision (PRECISION) << vo.GetAbsMin();
+ else if (operation == "absmax")
+ _tmp_output << setprecision (PRECISION) << vo.GetAbsMax();
+ else if (operation == "mode")
+ _tmp_output << vo.GetMode();
+ else if (operation == "antimode")
+ _tmp_output << vo.GetAntiMode();
+ else if (operation == "count")
+ _tmp_output << setprecision (PRECISION) << vo.GetCount();
+ else if (operation == "count_distinct")
+ _tmp_output << setprecision (PRECISION) << vo.GetCountDistinct();
+ else if (operation == "collapse")
+ _tmp_output << vo.GetCollapse();
+ else if (operation == "distinct")
+ _tmp_output << vo.GetDistinct();
+ else {
+ cerr << "ERROR: " << operation << " is an unrecognized operation\n";
+ exit(1);
+ }
+ _output.append(_tmp_output.str());
+
+}
diff --git a/src/mapBed/mapBed.h b/src/mapFile/mapFile.h
similarity index 65%
rename from src/mapBed/mapBed.h
rename to src/mapFile/mapFile.h
index f8cc5de..cb1da08 100644
--- a/src/mapBed/mapBed.h
+++ b/src/mapFile/mapFile.h
@@ -1,5 +1,5 @@
/*****************************************************************************
- mapBed.h
+ mapFile.h
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -9,9 +9,54 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#ifndef MAPBED_H
-#define MAPBED_H
+#ifndef MAPFILE_H
+#define MAPFILE_H
+using namespace std;
+
+#include <sstream>
+#include <iomanip>
+#include "VectorOps.h"
+#include "RecordKeyList.h"
+
+using namespace std;
+
+class ContextMap;
+class BlockMgr;
+class RecordOutputMgr;
+
+class FileMap {
+
+public:
+ FileMap(ContextMap *context);
+ ~FileMap(void);
+
+ bool mapFiles();
+
+private:
+ ContextMap *_context;
+ Record *_queryRec;
+ Record *_databaseRec;
+ BlockMgr *_blockMgr;
+ RecordOutputMgr *_recordOutputMgr;
+
+ vector<string> _column_vec; // vector to hold current column's worth of data
+
+ ostringstream _tmp_output;
+ QuickString _output; // placeholder for the results of mapping B to each a in A.
+ //------------------------------------------------
+ // private methods
+ //------------------------------------------------
+ void Map();
+ void SummarizeHits(RecordKeyList &hits);
+ void ExtractColumnFromHits(RecordKeyList &hits);
+
+};
+
+#endif /* MAPFILE_H */
+
+
+/*
#include "bedFile.h"
#include "chromsweep.h"
#include "VectorOps.h"
@@ -75,5 +120,5 @@ private:
string MapHits(const BED &a, const vector<BED> &hits);
void ExtractColumnFromHits(const vector<BED> &hits);
};
-
-#endif /* MAPBED_H */
+*/
+//#endif /* MAPFILE_H */
diff --git a/src/mapBed/mapMain.cpp b/src/mapFile/mapMain.cpp
similarity index 88%
rename from src/mapBed/mapMain.cpp
rename to src/mapFile/mapMain.cpp
index 8f1559d..a9eeb36 100644
--- a/src/mapBed/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -9,21 +9,37 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "mapBed.h"
-#include "version.h"
-
using namespace std;
+#include "mapFile.h"
+#include "ContextMap.h"
+
// define our program name
#define PROGRAM_NAME "bedtools map"
+void map_help(void);
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+int map_main(int argc, char* argv[]) {
-// function declarations
-void map_help(void);
+ ContextMap *context = new ContextMap();
+ if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+ if (!context->getErrorMsg().empty()) {
+ cerr << context->getErrorMsg() << endl;
+ }
+ map_help();
+ delete context;
+ return 0;
+ }
+ FileMap *fileMap = new FileMap(context);
+
+ bool retVal = fileMap->mapFiles();
+ delete fileMap;
+ delete context;
+ return retVal ? 0 : 1;
+}
+
+/*
int map_main(int argc, char* argv[]) {
// our configuration variables
@@ -158,6 +174,7 @@ int map_main(int argc, char* argv[]) {
return 0;
}
}
+*/
void map_help(void) {
@@ -174,7 +191,7 @@ void map_help(void) {
cerr << "\t-o\t" << "Specify the operation that should be applied to -c." << endl;
cerr << "\t\t Valid operations:" << endl;
- cerr << "\t\t sum, min, max," << endl;
+ cerr << "\t\t sum, min, max, absmin, absmax," << endl;
cerr << "\t\t mean, median," << endl;
cerr << "\t\t collapse (i.e., print a comma separated list (duplicates allowed)), " << endl;
cerr << "\t\t distinct (i.e., print a comma separated list (NO duplicates allowed)), " << endl;
@@ -198,6 +215,11 @@ void map_help(void) {
cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+ cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
+ cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
+ cerr <<"\t\tacross input files." << endl << endl;
+
cerr << "\t-null\t" << "The value to print if no overlaps are found for an A interval." << endl;
cerr << "\t\t- Default - \".\"" << endl << endl;
diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp
index 0c1bb27..dae9887 100644
--- a/src/mergeBed/mergeBed.cpp
+++ b/src/mergeBed/mergeBed.cpp
@@ -21,7 +21,7 @@ void BedMerge::ReportMergedNames(const vector<string> &names) {
vector<string>::const_iterator nameEnd = names.end();
for (; nameItr != nameEnd; ++nameItr) {
if (nameItr < (nameEnd - 1))
- cout << *nameItr << ";";
+ cout << *nameItr << _delimiter;
else
cout << *nameItr;
}
@@ -29,7 +29,9 @@ void BedMerge::ReportMergedNames(const vector<string> &names) {
else {
cerr << endl
<< "*****" << endl
- << "*****ERROR: No names found to report for the -names option. Exiting." << endl
+ << "*****ERROR: "
+ << "No names found to report for the -names option. Exiting."
+ << endl
<< "*****" << endl;
exit(1);
}
@@ -58,7 +60,7 @@ void BedMerge::ReportMergedScores(const vector<string> &scores) {
else if (_scoreOp == "antimode")
buffer << setprecision (PRECISION) << vo.GetAntiMode();
else if (_scoreOp == "collapse")
- buffer << setprecision (PRECISION) << vo.GetCollapse();
+ buffer << setprecision (PRECISION) << vo.GetCollapse(_delimiter);
cout << "\t" << buffer.str();
}
else {
@@ -79,14 +81,16 @@ BedMerge::BedMerge(string &bedFile,
bool forceStrand,
bool reportNames,
bool reportScores,
- const string &scoreOp) :
+ const string &scoreOp,
+ const string &delimiter) :
_bedFile(bedFile),
_numEntries(numEntries),
_forceStrand(forceStrand),
_reportNames(reportNames),
_reportScores(reportScores),
_scoreOp(scoreOp),
- _maxDistance(maxDistance)
+ _maxDistance(maxDistance),
+ _delimiter(delimiter)
{
_bed = new BedFile(bedFile);
@@ -182,12 +186,12 @@ void BedMerge::ReportStranded(string chrom, int start,
// just the merged intervals
if (_numEntries == false && _reportNames == false &&
_reportScores == false) {
- printf("\t%s\n", strand.c_str());
+ printf("\t\t\t%s\n", strand.c_str());
}
// merged intervals and counts
else if (_numEntries == true && _reportNames == false &&
_reportScores == false) {
- printf("\t%d\t%s\n", mergeCount, strand.c_str());
+ printf("\t\t%d\t%s\n", mergeCount, strand.c_str());
}
// merged intervals, counts, and scores
else if (_numEntries == true && _reportNames == false &&
@@ -215,11 +219,12 @@ void BedMerge::ReportStranded(string chrom, int start,
else if (_numEntries == false && _reportNames == true &&
_reportScores == false) {
ReportMergedNames(names);
- printf("\t%s\n", strand.c_str());
+ printf("\t.\t%s\n", strand.c_str());
}
// merged intervals and scores
else if (_numEntries == false && _reportNames == false &&
_reportScores == true) {
+ printf("\t");
ReportMergedScores(scores);
printf("\t%s\n", strand.c_str());
}
diff --git a/src/mergeBed/mergeBed.h b/src/mergeBed/mergeBed.h
index 52eb7cb..d9b0c14 100644
--- a/src/mergeBed/mergeBed.h
+++ b/src/mergeBed/mergeBed.h
@@ -34,7 +34,8 @@ public:
// constructor
BedMerge(string &bedFile, bool numEntries,
int maxDistance, bool forceStrand,
- bool reportNames, bool reportScores, const string &scoreOp);
+ bool reportNames, bool reportScores,
+ const string &scoreOp, const string &delimiter);
// destructor
~BedMerge(void);
@@ -51,11 +52,20 @@ private:
bool _reportScores;
string _scoreOp;
int _maxDistance;
+ string _delimiter;
// instance of a bed file class.
BedFile *_bed;
- void Report(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount);
- void ReportStranded(string chrom, int start, int end, const vector<string> &names, const vector<string> &scores, int mergeCount, string strand);
+ void Report(string chrom, int start, int end,
+ const vector<string> &names,
+ const vector<string> &scores,
+ int mergeCount);
+
+ void ReportStranded(string chrom, int start, int end,
+ const vector<string> &names,
+ const vector<string> &scores,
+ int mergeCount,
+ string strand);
void ReportMergedNames(const vector<string> &names);
void ReportMergedScores(const vector<string> &scores);
diff --git a/src/mergeBed/mergeMain.cpp b/src/mergeBed/mergeMain.cpp
index 2f1a164..28b869a 100644
--- a/src/mergeBed/mergeMain.cpp
+++ b/src/mergeBed/mergeMain.cpp
@@ -41,6 +41,7 @@ int merge_main(int argc, char* argv[]) {
bool forceStrand = false;
bool reportNames = false;
bool reportScores = false;
+ string delimiter = ",";
for(int i = 1; i < argc; i++) {
int parameterLength = (int)strlen(argv[i]);
@@ -87,6 +88,12 @@ int merge_main(int argc, char* argv[]) {
i++;
}
}
+ else if (PARAMETER_CHECK("-delim", 6, parameterLength)) {
+ if ((i+1) < argc) {
+ delimiter = argv[i + 1];
+ i++;
+ }
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -98,15 +105,28 @@ int merge_main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
showHelp = true;
}
- if ((reportScores == true) && (scoreOp != "sum") && (scoreOp != "max") && (scoreOp != "min") && (scoreOp != "mean") &&
- (scoreOp != "mode") && (scoreOp != "median") && (scoreOp != "antimode") && (scoreOp != "collapse"))
+ if ((reportScores == true) && (scoreOp != "sum")
+ && (scoreOp != "max") && (scoreOp != "min")
+ && (scoreOp != "mean") && (scoreOp != "mode")
+ && (scoreOp != "median") && (scoreOp != "antimode")
+ && (scoreOp != "collapse"))
{
- cerr << endl << "*****" << endl << "*****ERROR: Invalid scoreOp selection \"" << scoreOp << endl << "\" *****" << endl;
+ cerr << endl
+ << "*****"
+ << endl
+ << "*****ERROR: Invalid scoreOp selection \""
+ << scoreOp
+ << endl
+ << "\" *****"
+ << endl;
showHelp = true;
}
if (!showHelp) {
- BedMerge *bm = new BedMerge(bedFile, numEntries, maxDistance, forceStrand, reportNames, reportScores, scoreOp);
+ BedMerge *bm = new BedMerge(bedFile, numEntries,
+ maxDistance, forceStrand,
+ reportNames, reportScores,
+ scoreOp, delimiter);
delete bm;
}
else {
@@ -137,7 +157,8 @@ void merge_help(void) {
cerr << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
cerr << "\t\t- (INTEGER)" << endl << endl;
- cerr << "\t-nms\t" << "Report the names of the merged features separated by semicolons." << endl << endl;
+ cerr << "\t-nms\t" << "Report the names of the merged features separated by commas." << endl;
+ cerr << "\t\tChange delim. with -delim." << endl << endl;
cerr << "\t-scores\t" << "Report the scores of the merged features. Specify one of " << endl;
cerr << "\t\tthe following options for reporting scores:" << endl;
@@ -146,6 +167,11 @@ void merge_help(void) {
cerr << "\t\t collapse (i.e., print a semicolon-separated list)," << endl;
cerr << "\t\t- (INTEGER)" << endl << endl;
+ cerr << "\t-delim\t" << "Specify a custom delimiter for the -nms and -scores concat options" << endl;
+ cerr << "\t\t- Example: -delim \"|\"" << endl;
+ cerr << "\t\t- Default: \",\"." << endl << endl;
+
+
cerr << "Notes: " << endl;
cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
cerr << "\t will in BED format with zero-based starts" << endl << endl;
diff --git a/src/multiIntersectBed/Makefile b/src/multiIntersectBed/Makefile
index 6ebf605..e43e755 100644
--- a/src/multiIntersectBed/Makefile
+++ b/src/multiIntersectBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/Point/ \
diff --git a/src/multiIntersectBed/multiIntersectBed.h b/src/multiIntersectBed/multiIntersectBed.h
index 949cea1..fb757a8 100644
--- a/src/multiIntersectBed/multiIntersectBed.h
+++ b/src/multiIntersectBed/multiIntersectBed.h
@@ -17,7 +17,7 @@
#include <vector>
#include <string>
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "Point.h"
class MultiIntersectBed
diff --git a/src/multiIntersectBed/multiIntersectBedMain.cpp b/src/multiIntersectBed/multiIntersectBedMain.cpp
index 3ac39d1..5b8d1b2 100644
--- a/src/multiIntersectBed/multiIntersectBedMain.cpp
+++ b/src/multiIntersectBed/multiIntersectBedMain.cpp
@@ -19,7 +19,7 @@
#include <getopt.h>
#include <libgen.h> //for basename()
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "multiIntersectBed.h"
#include "version.h"
diff --git a/src/nekSandbox1/FormatGuess.h b/src/nekSandbox1/FormatGuess.h
new file mode 100644
index 0000000..0519500
--- /dev/null
+++ b/src/nekSandbox1/FormatGuess.h
@@ -0,0 +1,76 @@
+///*
+// * FormatGuess.h
+// *
+// * Created on: Mar 11, 2013
+// * Author: nek3d
+// */
+//
+//#ifndef FORMATGUESS_H_
+//#define FORMATGUESS_H_
+//
+//#include "PushBackStream.h"
+//
+//class FormatGuess
+//{
+// std::string name;
+//public:
+// FormatGuess(const char* name)
+// :name(name)
+// {}
+// const char* format() const
+// {
+// return name.c_str();
+// }
+// virtual bool guess(PushBackStreamBuf* buf)=0;
+//};
+//
+//class VCFGuess:public FormatGuess
+//{
+//public:
+// VCFGuess()
+// :FormatGuess("VCF")
+// {}
+//
+// virtual bool guess(PushBackStreamBuf* buf)
+// {
+// const std::string fileformat("##fileformat=");
+// bool is_vcf=true;
+// std::ostringstream os;
+// for(std::size_t i=0;i< fileformat.size();++i)
+// {
+// int c=buf->sbumpc();
+// if(c!=-1) os << (char)c;
+// if(c!=fileformat[i]) {is_vcf=false;break;}
+// }
+// buf->push_back(os.str());
+// return is_vcf;
+// }
+//};
+//
+//
+//class XMLGuess:public FormatGuess
+//{
+//public:
+//
+// XMLGuess()
+// :FormatGuess("XML")
+// {}
+//
+// virtual bool guess(PushBackStreamBuf* buf)
+// {
+// const std::string xmlheader("<?xml ");
+// bool is_xml=true;
+// std::ostringstream os;
+// for(std::size_t i=0;i< xmlheader.size();++i)
+// {
+// int c=buf->sbumpc();
+// if(c!=-1) os << (char)c;
+// if(c!=xmlheader[i]) {is_xml=false;break;}
+// }
+// buf->push_back(os.str());
+// return is_xml;
+// }
+//};
+//
+//
+//#endif /* FORMATGUESS_H_ */
diff --git a/src/mapBed/Makefile b/src/nekSandbox1/Makefile
similarity index 52%
rename from src/mapBed/Makefile
rename to src/nekSandbox1/Makefile
index 96828e6..fbe6d86 100644
--- a/src/mapBed/Makefile
+++ b/src/nekSandbox1/Makefile
@@ -5,23 +5,28 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
- -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records \
+ -I$(UTILITIES_DIR)/general \
+ -I$(UTILITIES_DIR)/NewChromsweep \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/BamTools/include \
- -I$(UTILITIES_DIR)/BamTools-Ancillary \
- -I$(UTILITIES_DIR)/chromsweep \
- -I$(UTILITIES_DIR)/VectorOps \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
+
+
+
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= mapMain.cpp mapBed.cpp mapBed.h
-OBJECTS= mapMain.o mapBed.o
+SOURCES= nekSandboxMain.cpp
+OBJECTS= nekSandboxMain.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= nekSandbox1
all: $(BUILT_OBJECTS)
@@ -30,9 +35,9 @@ all: $(BUILT_OBJECTS)
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-
+
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/mapMain.o $(OBJ_DIR)/mapBed.o
+ @rm -f $(OBJ_DIR)/nekSandboxMain.o
.PHONY: clean
diff --git a/src/nekSandbox1/nekSandboxMain.cpp b/src/nekSandbox1/nekSandboxMain.cpp
new file mode 100644
index 0000000..ac3fb31
--- /dev/null
+++ b/src/nekSandbox1/nekSandboxMain.cpp
@@ -0,0 +1,338 @@
+using namespace std;
+
+#include "ContextIntersect.h"
+#include "FileRecordMgr.h"
+#include <iostream>
+#include <cstdio>
+#include "RecordKeyList.h"
+#include "NewChromsweep.h"
+#include "DualQueue.h"
+#include "ParseTools.h"
+#include <sstream>
+#include <iomanip>
+//#include "FormatGuess.h"
+
+#include "PushBackStreamBuf.h"
+#include "InflateStreamBuf.h"
+#include "InputStreamMgr.h"
+#include "BufferedStreamMgr.h"
+#include "api/internal/io/BgzfStream_p.h"
+
+//void doSweep(const Context *context);
+//void testDualQueue(Context *context);
+//
+//void test_streams();
+
+
+using namespace std;
+
+int nek_sandbox1_main2(int argc,char** argv);
+
+int nek_sandbox1_main(int argc,char** argv)
+{
+
+// for (int i=0; i < 4000; i++) {
+// cout << "# This is line " << i << " of a file with a large header." << endl;
+// }
+// return 0;
+
+ if (argc < 2) {
+ cerr << "Error: Need one input file. Use \"-\" for stdin." << endl;
+ }
+// ifstream inFileStream(argv[1]);
+// static const int BUF_SIZE = 8192;
+// BamTools::Internal::BgzfStream bgStream;
+// bgStream.OpenStream(&inFileStream, BamTools::IBamIODevice::ReadOnly);
+// char sLine[BUF_SIZE];
+// while (bgStream.IsOpen()) {
+// memset(sLine, 0, BUF_SIZE);
+// bgStream.Read(sLine, BUF_SIZE-1);
+// if((int)strlen(sLine) < BUF_SIZE-1) {
+// bgStream.Close();
+// }
+// printf("%s", sLine);
+// }
+// return 0;
+// QuickString filename(argv[1]);
+// istream *inputStream = NULL;
+// if (filename == "-") {
+// inputStream = &cin;
+// } else {
+// inputStream = new ifstream(filename.c_str());
+// }
+//
+// BamTools::BamReader _bamReader;
+// try {
+// _bamReader.OpenStream(inputStream);
+// }
+// catch (...) {
+// fprintf(stderr, "ERROR: Unable to open BAM file from standard input.\n");
+// exit(1);
+// }
+//// try {
+//// _bamReader.Open(argv[1]);
+//// }
+//// catch (...) {
+//// fprintf(stderr, "ERROR: Unable to open BAM file %s\n",argv[1]);
+//// exit(1);
+//// }
+//// }
+// QuickString _bamHeader = _bamReader.GetHeaderText();
+// BamTools::RefVector _references = _bamReader.GetReferenceData();
+//
+// if (_bamHeader.empty() || _references.empty()) {
+// cout << "This is not a bam file." << endl;
+// } else {
+// cout << "This is a BAM file." << endl;
+// }
+// return 0;
+//
+// ifstream myFile(argv[1]);
+// if (!myFile.good()) {
+// cerr << "Error: Can't open genome file" << argv[1] << "Exiting..." << endl;
+// exit(1);
+// }
+// string sLine;
+// vector<QuickString> fields;
+// QuickString chrName;
+//
+// vector<QuickString> chroms;
+// chroms.push_back("1");
+// chroms.push_back("2");
+// chroms.push_back("10");
+// chroms.push_back("11");
+//
+// vector<int> chromCounts(4, 0);
+// int chromIdx = 0;
+// while (!myFile.eof()) {
+// sLine.clear();
+// fields.clear();
+// getline(myFile, sLine);
+// if (sLine[0] == '@') {
+// cout << sLine << endl;
+// continue;
+// }
+// Tokenize(sLine.c_str(), fields);
+// const QuickString &currChrom = fields[2];
+// if (currChrom == chroms[chromIdx]) {
+// cout << sLine << endl;
+// chromCounts[chromIdx]++;
+// if (chromCounts[chromIdx] >= 3000) {
+// chromIdx++;
+// }
+// if (chromIdx > 3) {
+// break;
+// }
+// }
+// }
+//
+// return 0;
+//
+// ContextIntersect context;
+// context.addInputFile(argv[1]);
+// context.setSortedInput(true);
+//// context.setObeySplits(true);
+//
+// FileRecordMgr frm(0, &context);
+//// frm.getBlockMgr()->setBreakOnSkipOps(true);
+// if (!frm.open()) {
+// cerr << "Error: couldn't open file " << argv[1] << ". Exiting." << endl;
+// exit(1);
+// }
+// cout << "File Type is : " << frm.getFileType() << ", " << frm.getFileTypeName() << "." << endl;
+// cout << "RecordType is : " << frm.getRecordType() << ", " << frm.getRecordTypeName() << "." << endl;
+//
+// bool headerFound = false;
+// QuickString outbuf;
+// while (!frm.eof()) {
+// Record *record = frm.allocateAndGetNextRecord();
+// if (!headerFound && frm.hasHeader()) {
+// cout << frm.getHeader() << endl;
+// headerFound = true;
+// }
+// if (record == NULL) {
+// break;
+// }
+//
+// outbuf.clear();
+// record->print(outbuf);
+// printf("%s\n", outbuf.c_str());
+//
+// RecordKeyList recList(record);
+// int blockCount = frm.getBlockMgr()->getBlocks(recList);
+// printf("The %d blocks are:\n", blockCount);
+// for (RecordKeyList::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
+// iter->value()->print();
+// printf("\n");
+// }
+// printf("\n\n");
+// frm.getBlockMgr()->deleteBlocks(recList);
+
+// frm.deleteRecord(record);
+// }
+// cout << "Final header is: " << frm.getHeader() << endl;
+// frm.close();
+
+ return 0;
+}
+
+//int nek_sandbox1_main2(int argc,char** argv)
+//{
+//
+//
+// vector<FormatGuess *> formats;
+// formats.push_back(new VCFGuess());
+// formats.push_back(new XMLGuess());
+//
+// PushBackStreamBuf pbs(std::cin.rdbuf());
+// std::istream in(&pbs);
+// const char* format=0;
+// for(size_t i=0;i< 2;++i)
+// {
+// if( formats[i]->guess(&pbs))
+// {
+// format=formats[i]->format();
+// break;
+// }
+// }
+// std::string line;
+// while(getline(in,line))
+// {
+// if(format!=0) cout << format << "\t";
+// cout << line << endl;
+// }
+// return 0;
+//}
+//
+#ifdef false
+int nek_sandbox1_main(int argc, char **argv) {
+
+
+
+ for (int i=0; i < argc; i ++) {
+ cout << "Arg " << i << " is: " << argv[i] << endl;
+ }
+ test_streams();
+ return 0;
+
+ /////////////////////////////////
+ //
+ // BLOCK FOR DUEL QUEUE
+ //
+ if (argc < 2) {
+ cerr << "Error: need at least one file name." << endl;
+ return 1;
+ }
+
+ Context *context = new Context();
+ context->addInputFile(argv[1]);
+ testDualQueue(context);
+ return 0;
+ //
+ ////////////////////////////////
+
+
+
+
+
+ /////////////////////////////////
+ //
+ // BLOCK FOR SWEEP
+ //
+
+ if (argc < 3) {
+ cerr << "Error: need at least two data file names." << endl;
+ return 1;
+ }
+
+ Context *context = new Context();
+ context->parseCmdArgs(argc, argv, 1);
+
+ doSweep(context);
+ return 0;
+ //
+ ////////////////////////////////
+
+}
+
+void doSweep(const char *file1, const char *file2, const string &genomeFile)
+{
+ Context *context = new Context();
+ context->addInputFile(file1);
+ context->addInputFile(file2);
+ context->openGenomeFile(genomeFile);
+
+ ChromSweep sweep = ChromSweep(context);
+
+ if (!sweep.init()) {
+ cerr << "ERROR: Failure to open files in jaccard's getIntersection method." << endl;
+ return;
+ }
+
+ RecordKeyList hit_set;
+ while (sweep.next(hit_set)) {
+// _intersectionVal += getTotalIntersection(&hit_set);
+ continue;
+ }
+ unsigned long unionVal = sweep.getQueryTotalRecordLength() + sweep.getDatabaseTotalRecordLength();
+ cout << endl << endl << "Union value is: " << unionVal << endl << endl;
+}
+
+void testDualQueue(Context *context) {
+ DualQueue<Record *, DualQueueAscending > dqAsc;
+// DualQueue<Record *, DualQueueDescending> dqDesc;
+
+ FileRecordMgr frm(context->getInputFileName(0), context);
+ frm.open();
+
+ printf("Original record order is:\n");
+ while (!frm.eof()) {
+ Record *record = frm.allocateAndGetNextRecord();
+ if (record == NULL) {
+ continue;
+ }
+// printf("\n\nNext Record is:\n");
+ record->print();
+ printf("\n");
+ dqAsc.push(record);
+// dqDesc.push(record);
+ }
+
+ printf("\nSupposedly ascending order is:\n");
+ while (!dqAsc.empty()) {
+ const Record *record = dqAsc.top();
+ dqAsc.pop();
+ record->print();
+ printf("\n");
+ }
+
+// printf("\nSupposedly descending order is:\n");
+// while (!dqDesc.empty()) {
+// const Record *record = dqDesc.top();
+// dqDesc.pop();
+// record->print();
+// printf("\n");
+// }
+ frm.close();
+}
+
+void test_streams()
+{
+ char myBuf[10];
+ memset(myBuf, 0, 10);
+
+ cin >> noskipws >> setw(9) >> myBuf;
+
+ stringstream newStream;
+ newStream << "myBuf =:" << myBuf << endl;
+
+ newStream << "Full stream was:" << endl;
+ newStream << myBuf;
+ newStream << cin.rdbuf();
+
+
+ cout << newStream.str() << endl;
+
+}
+
+#endif //ifdef false
diff --git a/src/nucBed/nucBed.cpp b/src/nucBed/nucBed.cpp
index 446f6a6..9b515d2 100644
--- a/src/nucBed/nucBed.cpp
+++ b/src/nucBed/nucBed.cpp
@@ -15,16 +15,17 @@
NucBed::NucBed(string &dbFile, string &bedFile, bool printSeq,
bool hasPattern, const string &pattern,
- bool forceStrand, bool ignoreCase)
+ bool forceStrand, bool ignoreCase, bool useFullHeader)
{
- _dbFile = dbFile;
- _bedFile = bedFile;
- _printSeq = printSeq;
- _hasPattern = hasPattern;
- _pattern = pattern;
- _forceStrand = forceStrand;
- _ignoreCase = ignoreCase;
+ _dbFile = dbFile;
+ _bedFile = bedFile;
+ _printSeq = printSeq;
+ _hasPattern = hasPattern;
+ _pattern = pattern;
+ _forceStrand = forceStrand;
+ _ignoreCase = ignoreCase;
+ _useFullHeader = useFullHeader;
_bed = new BedFile(_bedFile);
// Compute the DNA content in each BED/GFF/VCF interval
@@ -109,7 +110,7 @@ void NucBed::ProfileDNA() {
// open and memory-map genome file
FastaReference fr;
bool memmap = true;
- fr.open(_dbFile, memmap);
+ fr.open(_dbFile, memmap, _useFullHeader);
bool headerReported = false;
BED bed;
diff --git a/src/nucBed/nucBed.h b/src/nucBed/nucBed.h
index ba45af4..dc82f3e 100644
--- a/src/nucBed/nucBed.h
+++ b/src/nucBed/nucBed.h
@@ -31,7 +31,7 @@ public:
// constructor
NucBed(string &dbFile, string &bedFile, bool printSeq,
bool hasPattern, const string &pattern,
- bool forceStrand, bool ignoreCase);
+ bool forceStrand, bool ignoreCase, bool useFullHeader);
// destructor
~NucBed(void);
@@ -46,6 +46,7 @@ private:
string _pattern;
bool _forceStrand;
bool _ignoreCase;
+ bool _useFullHeader;
// instance of a bed file class.
BedFile *_bed;
diff --git a/src/nucBed/nucBedMain.cpp b/src/nucBed/nucBedMain.cpp
index eff8bec..c37212a 100644
--- a/src/nucBed/nucBedMain.cpp
+++ b/src/nucBed/nucBedMain.cpp
@@ -35,12 +35,13 @@ int nuc_main(int argc, char* argv[]) {
string pattern;
// checks for existence of parameters
- bool haveFastaDb = false;
- bool haveBed = false;
- bool printSeq = false;
- bool hasPattern = false;
- bool forceStrand = false;
- bool ignoreCase = false;
+ bool haveFastaDb = false;
+ bool haveBed = false;
+ bool printSeq = false;
+ bool hasPattern = false;
+ bool forceStrand = false;
+ bool ignoreCase = false;
+ bool useFullHeader = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -90,6 +91,9 @@ int nuc_main(int argc, char* argv[]) {
pattern = argv[i + 1];
i++;
}
+ }
+ else if(PARAMETER_CHECK("-fullHeader", 11, parameterLength)) {
+ useFullHeader = true;
}
else {
cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
@@ -104,7 +108,8 @@ int nuc_main(int argc, char* argv[]) {
if (!showHelp) {
NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq,
- hasPattern, pattern, forceStrand, ignoreCase);
+ hasPattern, pattern, forceStrand, ignoreCase,
+ useFullHeader);
delete nuc;
}
else {
@@ -134,8 +139,12 @@ void nuc_help(void) {
cerr << "\t-pattern\tReport the number of times a user-defined sequence" << endl;
cerr << "\t\t\tis observed (case-sensitive)." << endl << endl;
- cerr << "\t-C\tIgore case when matching -pattern. By defaulty, case matters." << endl << endl;
-
+ cerr << "\t-C\tIgnore case when matching -pattern. By defaulty, case matters." << endl << endl;
+
+ cerr << "\t-fullHeader\tUse full fasta header." << endl;
+ cerr << "\t\t- By default, only the word before the first space or tab "
+ << "is used." << endl << endl;
+
cerr << "Output format: " << endl;
cerr << "\tThe following information will be reported after each BED entry:" << endl;
cerr << "\t 1) %AT content" << endl;
diff --git a/src/pairToBed/pairToBedMain.cpp b/src/pairToBed/pairToBedMain.cpp
index 740aaac..8d5a585 100644
--- a/src/pairToBed/pairToBedMain.cpp
+++ b/src/pairToBed/pairToBedMain.cpp
@@ -178,7 +178,7 @@ void pairtobed_help(void) {
cerr << "Options: " << endl;
- cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl;
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well. Replaces -a." << endl;
cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
diff --git a/src/randomBed/Makefile b/src/randomBed/Makefile
index 3a9ee89..2c795c2 100644
--- a/src/randomBed/Makefile
+++ b/src/randomBed/Makefile
@@ -5,7 +5,7 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/genomeFile/ \
+INCLUDES = -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/version/
diff --git a/src/randomBed/randomBed.h b/src/randomBed/randomBed.h
index f922a38..4002c19 100644
--- a/src/randomBed/randomBed.h
+++ b/src/randomBed/randomBed.h
@@ -9,7 +9,7 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/regressTest/Makefile b/src/regressTest/Makefile
new file mode 100644
index 0000000..e9ceebf
--- /dev/null
+++ b/src/regressTest/Makefile
@@ -0,0 +1,49 @@
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/lineFileUtilities/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src \
+ -I$(UTILITIES_DIR)/version/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records \
+ -I$(UTILITIES_DIR)/general
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
+#OBJECTS= regressTestMain.o RegressTest.o
+#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= regressTest
+
+
+all: #$(BUILT_OBJECTS)
+ @echo "compiling RegressTest.cpp"
+ @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+ @echo "compiling regressTestMain.cpp"
+ @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+.PHONY: all
+
+#$(BUILT_OBJECTS): $(SOURCES)
+# @echo " * compiling" $(*F).cpp
+# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/regressTestMain.o $(OBJ_DIR)/regressTest.o
+
+.PHONY: clean
diff --git a/src/regressTest/RegressTest.cpp b/src/regressTest/RegressTest.cpp
new file mode 100644
index 0000000..3b67925
--- /dev/null
+++ b/src/regressTest/RegressTest.cpp
@@ -0,0 +1,664 @@
+#include "RegressTest.h"
+#include <cstdlib>
+#include "SingleLineDelimTextFileReader.h"
+#include "BufferedStreamMgr.h"
+#include "lineFileUtilities.h"
+#include "ParseTools.h"
+#include <sys/stat.h>
+#include <ctime>
+
+const string RegressTest::_hardOptsCmd = "HARD_OPTIONS";
+const string RegressTest::_correctCmd = "CORRECT";
+const string RegressTest::_performCmd = "PERFORM";
+const string RegressTest::_randomCmd = "RANDOM";
+
+const string RegressTest::_space = " ";
+const string RegressTest::_redirect = " > ";
+const string RegressTest::_devNull = " /dev/null ";
+//const string RegressTest::_bedOpsCmd = "/home/nek3d/testWorkspace/bedops/bin/bedmap --echo --echo-map --bp-ovr 1 ";
+const string RegressTest::_bedOpsCmd = "/home/nek3d/testWorkspace/bedops/bin/bedops --intersect ";
+
+
+RegressTest::RegressTest()
+: _filesPerRun(0),
+ _generatedFileNumber(1),
+ _isOldProgBedops(false)
+{
+ _correctFiles = new fileListType();
+ _performFiles = new fileListType();
+}
+
+RegressTest::~RegressTest()
+{
+
+ delete _correctFiles;
+ _correctFiles = NULL;
+
+ delete _performFiles;
+ _performFiles = NULL;
+}
+
+bool RegressTest::init(int argc, char **argv)
+{
+ //TBD: Perhaps allow option for specifying report file.
+ _fpReportFile = stdout;
+
+ if (!parseParams(argc, argv)) {
+ return false;
+ }
+
+ //make banner title for report
+ fprintf(_fpReportFile, "\n\n***********************************************************\n\n");
+ fprintf(_fpReportFile, "REGRESSION TEST FOR BEDTOOLS SUB-PROGRAM: %s\n", _subProgram.c_str());
+ fprintf(_fpReportFile, "\n***********************************************************\n\n");
+
+
+ //setup output directory for testing's temporary files and generated data files.
+ _tmpDirname = "tempTesting_";
+ time_t currTime = time(NULL);
+ string timeStr = ctime(&currTime); //timeStr will equal Www Mmm dd hh:mm:ss yyyy followed by newline and null char.
+ //chomp the newLine
+ timeStr.erase(timeStr.size()-1);
+ //adjust timeStr to change spaces to underscores.
+ for (int i=0; i < (int)timeStr.size(); i++) {
+ if (isspace(timeStr[i])) {
+ timeStr[i] = '_';
+ } else if (timeStr[i] == ':') {
+ timeStr[i] = '-';
+ }
+ }
+ _tmpDirname += timeStr;
+ int mkdirRetval = mkdir(_tmpDirname.c_str(), S_IRWXU | S_IRWXG | S_IRWXO ); //mkdir directory with all permissions allowed.
+ if (mkdirRetval != 0) {
+ fprintf(stderr, "Error: Unable to create temporary output directory %s.\n", _tmpDirname.c_str());
+ return false;
+ }
+ _tmpDirname += "/";
+
+ _memoryLogfilename = _tmpDirname + "memoryLog.txt";
+
+ _userName = getenv("USER");
+
+ if ((int)_filePrecessorOptions.size() != _filesPerRun) {
+ fprintf(stderr, "Error: Sub-program specific filesPerRun number must match number of precessor options.\n");
+ return false;
+ }
+
+ if (!config()) {
+ return false;
+ }
+
+ if ((int)_correctFiles->size() % _filesPerRun != 0) {
+ fprintf(stderr, "Error: number of correctness files is not evenly divisible by number of files per run.\n");
+ return false;
+ }
+
+ if ((int)_performFiles->size() % _filesPerRun != 0) {
+ fprintf(stderr, "Error: number of performance files is not evenly divisible by number of files per run.\n");
+ return false;
+ }
+
+ return true;
+}
+
+bool RegressTest::runTests() {
+ echoOptions();
+
+ //All set with set-up. Let's work some mojo.
+ if (!performTests(true)) {
+ fprintf(stderr, "Error: Failure in correctness tests.\n");
+ return false;
+ }
+
+ if (!performTests(false)) {
+ fprintf(stderr, "Error: Failure in performance tests.\n");
+ return false;
+ }
+
+ return true;
+
+}
+
+bool RegressTest::parseParams(int argc, char **argv)
+{
+ //usage: bedtools devtest sub-prog targetVersion configFile [optionsToTest]
+ if (argc < 5) {
+ usage();
+ return false;
+ }
+ _newVersion = argv[0];
+ _subProgram = argv[2];
+
+ _oldVersion = argv[3];
+ if (_oldVersion.find("bedops") != string::npos) {
+ _isOldProgBedops = true;
+ }
+
+
+ _configFilename = argv[4];
+
+ //special: add a blank option to the softOptions, so that performTests will compare
+ //runs with each soft opt to a run with no soft ops.
+ _softOptions.push_back("");
+ for (int i=5; i < argc; i++ ) {
+ _softOptions.push_back(argv[i]);
+ }
+ return true;
+}
+
+void RegressTest::usage() const {
+ fprintf(stderr, "Usage: bedtools regresstest sub-prog targetVersion configFile [optionsToTest]\n");
+}
+
+void RegressTest::echoOptions() const
+{
+ //show all command line and config file options and files
+ fprintf(_fpReportFile, "\nCONFIGURATION AND OPTIONS ARE:\n\n");
+ fprintf(_fpReportFile, "New Version: %s\n", _newVersion.c_str());
+ fprintf(_fpReportFile, "Old Version: %s\n\n", _oldVersion.c_str());
+ fprintf(_fpReportFile, "hardOptions: %s\n\n", _hardOptions.c_str());
+
+ for (int i=1; i < (int)_softOptions.size(); i++) {
+ fprintf(_fpReportFile, "SoftOption %d: %s\n", i, _softOptions[i].c_str());
+ }
+
+ fprintf(_fpReportFile, "\nFiles per run: %d\n", _filesPerRun);
+ for (int i=0; i < (int)_filePrecessorOptions.size(); i++) {
+ fprintf(_fpReportFile, "Precessor option %d: %s\n", i+1, _filePrecessorOptions[i].c_str());
+ }
+
+ for (int i=0; i < 2; i++) {
+ fileListType *fileList = i == 0 ? _correctFiles : _performFiles;
+ fprintf(_fpReportFile, "\n\n\%s TEST FILES:\n", i ==0 ? "CORRECTNESS" : "PERFORMANCE");
+ for (fileListType::const_iterator iter = fileList->begin(); iter != fileList->end(); iter++) {
+
+ const string &filename = iter->first;
+ const string &desc = iter->second;
+ fprintf(_fpReportFile, "\nFilename: %s\n", filename.c_str());
+ fprintf(_fpReportFile, "Description: %s\n", desc.c_str());
+ }
+ }
+}
+
+bool RegressTest::config() {
+ //Set hard options, populate correctness and performance file vectors by reading a config file
+
+ _configFile.open(_configFilename.c_str());
+ if (!_configFile.good()) {
+ cerr << "Error: unable to open config file " << _configFilename << endl;
+ }
+ vector<string> fields;
+ bool parseStatus = false;
+ int numLinesToRead = 0;
+ int linesRead = 0;
+ string sLine;
+ while (!_configFile.eof()) {
+ sLine.clear();
+ getline(_configFile, sLine);
+ fields.clear();
+
+ Tokenize(sLine, fields);
+ if (fields.size() != 2) {
+ continue;
+ }
+
+ const string &field1 = fields[0];
+ const string &field2 = fields[1];
+
+ if (field1 == _hardOptsCmd) {
+ _hardOptions = field2.c_str();
+ continue;
+ } else if (field1 == _correctCmd || field1 == _performCmd) {
+ numLinesToRead = atoi(field2.c_str());
+ if (field1 == _correctCmd) {
+ parseStatus = parseConfigLines(numLinesToRead, true);
+ } else {
+ parseStatus = parseConfigLines(numLinesToRead, false);
+ }
+ if (!parseStatus) {
+ fprintf(stderr, "Error: failed to read and parse requested %d lines for %s\n",
+ numLinesToRead, field1 == _correctCmd ? "Correctness tests" : "Performance tests");
+ _configFile.close();
+ return false;
+ } else {
+ linesRead += numLinesToRead;
+ }
+ } else {
+ fprintf(stderr, "Error: Malformed config file %s\n.\tCheck that num files specified matches num provided.\n", _configFilename.c_str());
+ _configFile.close();
+ return false;
+ }
+ }
+ if (linesRead == 0) {
+ fprintf(stderr, "Error: No file lines read in config file %s\n", _configFilename.c_str());
+ _configFile.close();
+ return false;
+ }
+
+ _configFile.close();
+ return true;
+}
+
+
+
+bool RegressTest::parseConfigLines(int numLinesToRead, bool correctnessFiles)
+{
+ string description;
+
+
+ fileListType *fileList = correctnessFiles ? _correctFiles : _performFiles;
+ string sLine;
+ vector<string> fields;
+ for (int i=0; i < numLinesToRead; i++) {
+
+ sLine.clear();
+ getline(_configFile, sLine);
+ fields.clear();
+
+ Tokenize(sLine, fields);
+ if (fields.size() != 2) {
+ continue;
+ }
+
+ const string &field1 = fields[0];
+ const string &field2 = fields[1];
+
+ if (field1 == _randomCmd) {
+ string genFilename;
+ if (!generateRandomFile(field2.c_str(), genFilename)) {
+ fprintf(stderr, "Error: could not generate random file with args: %s\n", field2.c_str());
+ return false;
+ }
+ description = _randomCmd + _space + field2.c_str();
+ fileList->push_back(make_pair(genFilename, description));
+ } else {
+ fileList->push_back(make_pair(field1.c_str(), field2.c_str()));
+ }
+ }
+ return true;
+}
+
+bool RegressTest::generateRandomFile(const string & randomArgs, string &filename)
+{
+ if (_generatedFileNumber == 1) { //first call, print banner to report
+ fprintf(_fpReportFile, "\nGENERATING TEST DATA:\n\n");
+ }
+
+
+ string genFilename = _tmpDirname + "generatedFile_";
+ string strNum;
+ int2str(_generatedFileNumber, strNum);
+ _generatedFileNumber++;
+
+ genFilename += strNum;
+ genFilename += ".bed";
+
+ //quick hack since v2.18 random currently doesn't support the -sort option in the random command
+ string genFileCmd = "~/testWorkspace/pfm3release/bin/bedtools"; //_newVersion;
+ genFileCmd += " random ";
+ string sortCmd = ""; //" | sort -k1,1 -nk2,2 "; Trouble getting pipes to work. Use -sorted command from now.
+ genFileCmd += randomArgs + sortCmd + _redirect + genFilename;
+
+ fprintf(_fpReportFile, "Creating data file %s with random args %s...\n", genFilename.c_str(), randomArgs.c_str());
+ if (system(genFileCmd.c_str()) != 0) { //expects successful calls to randomBed to return zero.
+ fprintf(_fpReportFile, "FAILED.\n");
+ filename.clear();
+ return false;
+ }
+ filename = genFilename;
+ fprintf(_fpReportFile, "Done.\n");
+ return true;
+}
+
+bool RegressTest::performTests(bool isCorrectnessTest)
+{
+ bool retval = true;
+ fileListType *fileList = isCorrectnessTest ? _correctFiles : _performFiles;
+ if (fileList->empty()) {
+ return true;
+ }
+ string inFilesCmd;
+ string baseCmd;
+ string allOptsCmd;
+ string finalCmd;
+ string oldVerionFinalCmd;
+ string newVersionFinalCmd;
+
+ int outFileCounter = 1;
+ string counterStr;
+ string outputBase = "tmp";
+ string outputSuffix = ".txt";
+ string outputFile = "/dev/null"; // /dev/null will be used for performance, but over-written for correctness
+
+
+ string bedOpsFileCmd; //special handling for bedops
+
+ string testType = isCorrectnessTest ? "CORRECTNESS" : "PERFORMANCE";
+ int testCounter = 0;
+ fprintf(_fpReportFile, "\n\n\n***********************************************************\n\n");
+ fprintf(_fpReportFile, "TESTS FOR %s\n", testType.c_str());
+ fprintf(_fpReportFile, "\n***********************************************************\n");
+
+ vector< fileListType::const_iterator> currFiles;
+ for (fileListType::const_iterator fileIter = fileList->begin(); fileIter != fileList->end(); fileIter += _filesPerRun) {
+ currFiles.clear();
+ string inFilesCmd = _space;
+ for (int i=0; i < _filesPerRun; i++) {
+ const string &infileName = (fileIter + i)->first;
+ inFilesCmd += _filePrecessorOptions[i] + _space + infileName + _space;
+ currFiles.push_back(fileIter + i);
+ }
+ if (_isOldProgBedops) {
+ bedOpsFileCmd = fileIter->first + _space + (fileIter + 1)->first + _space;
+ }
+ for (int i=0; i < (int)_softOptions.size(); i++ ) {
+ const string &softOpt = _softOptions[i];
+
+ //stop to report what test we're going to do.
+ testCounter++;
+ fprintf(_fpReportFile, "\n%s TEST %d\n\n", testType.c_str(), testCounter);
+ fprintf(_fpReportFile, "\tInput Files:\n");
+ for (int j=0; j < (int)currFiles.size(); j++) {
+ fprintf(_fpReportFile, "\tName: %s\n", currFiles[j]->first.c_str());
+ fprintf(_fpReportFile, "\tDesc: %s\n\n", currFiles[j]->second.c_str());
+ }
+ fprintf(_fpReportFile, "\tSoft option in use: %s\n", softOpt.empty() ? "NONE" : softOpt.c_str());
+ fprintf(_fpReportFile, "\n\tCommands to run:\n");
+ fileListType cmdAndOutput;
+ for (int j=0; j < 2; j++) { //loop through the two versions, old and new
+ const string &mainProg = j == 0 ? _oldVersion : _newVersion;
+ if (j==1 || !_isOldProgBedops) {
+ baseCmd = mainProg + _space + _subProgram + _space + inFilesCmd + _hardOptions + _space + softOpt + _redirect;
+ } else {
+ baseCmd = /*mainProg + _space + */ _bedOpsCmd + bedOpsFileCmd + _redirect;
+ }
+
+ //now we just need tmp output for correctness, or clock and memory footprinting for performance
+ if (isCorrectnessTest) {
+ int2str(outFileCounter, counterStr);
+ outFileCounter++;
+ outputFile = _tmpDirname + outputBase + counterStr + outputSuffix;
+ }
+
+ finalCmd = baseCmd + outputFile;
+ fprintf(_fpReportFile, "\t%s\n", finalCmd.c_str());
+ cmdAndOutput.push_back(make_pair(finalCmd, outputFile));
+ }
+ if (isCorrectnessTest) {
+ bool compStatus = executeAndCompareCorrectness(cmdAndOutput);
+ retval = retval && compStatus;
+ } else {
+ bool compStatus = executeAndComparePerformance(cmdAndOutput);
+ retval = retval && compStatus;
+ }
+ }
+ }
+
+ return retval;
+
+}
+
+bool RegressTest::executeAndCompareCorrectness(const fileListType &fileList) {
+ const string &cmd1 =fileList[0].first;
+ const string &output1 = fileList[0].second;
+ const string &cmd2 = fileList[1].first;
+ const string &output2 = fileList[1].second;
+
+// printf("\nRun correctness test: %s\n%s\n%s\n%s\n", cmd1.c_str(), output1.c_str(), cmd2.c_str(), output2.c_str());
+// return true;
+
+ int ret1 = system(cmd1.c_str());
+ if (ret1 !=0) {
+ fprintf(stderr, "\nError: received non-zero exit code %d from old version.\n", ret1);
+ return false;
+ }
+
+ int ret2 = system(cmd2.c_str());
+
+ if (ret2 !=0) {
+ fprintf(stderr, "\nError: received non-zero exit code %d from new version.\n", ret2);
+ return false;
+ }
+
+ //Here: implement a way to test differences in output. In the future, may wish to actually read the records
+ //and determine equivalence, i.e. same value for core fields chrName, start, end, name, score, strand.
+ //Right now, just use diff command, ensure output of diff is empty.
+
+ string diffFilename = _tmpDirname + "diffOut.txt";
+ string diffCmd = "diff ";
+ diffCmd += output1 + _space + output2 + _redirect + diffFilename;
+
+ system(diffCmd.c_str());
+
+ //now need to check for empty diffFile.
+ struct stat buf ;
+ int i;
+
+ i = stat(diffFilename.c_str(), &buf);
+ if (i!=0) {
+ fprintf(stderr, "Error: can't get status of diff output file %s\n", diffFilename.c_str()) ;
+ return false;
+ }
+
+ if (buf.st_size > 0) {
+ fprintf(_fpReportFile, "\n\tFAILED. Output files are different.\n");
+ return true;
+ }
+
+ fprintf(_fpReportFile, "\n\tPASSED. Output files are identical.\n");
+ return true;
+}
+
+bool RegressTest::executeAndComparePerformance(const fileListType &fileList) {
+ const string &cmd1 =fileList[0].first;
+// const string &output1 = fileList[0].second;
+ const string &cmd2 = fileList[1].first;
+// const string &output2 = fileList[1].second;
+
+// printf("\nRun performance test: %s\n%s\n%s\n%s\n", cmd1.c_str(), output1.c_str(), cmd2.c_str(), output2.c_str());
+// return true;
+
+ bool cmd1IsBedops = cmd1.find("bedops") != string::npos;
+ bool cmd2IsBedops = cmd2.find("bedops") != string::npos;
+
+ char timeBuf[100]; //be sure to initialize before use.
+ //run and time old version
+ fprintf(_fpReportFile, "\n\tRunning first command...\n");
+
+
+ startMemoryProfile(cmd1IsBedops);
+
+ time_t oldStartTime = time(NULL);
+ int ret1 = system(cmd1.c_str());
+ if (ret1 !=0) {
+ fprintf(stderr, "\nError: received non-zero exit code %d from old version.\n", ret1);
+ return false;
+ }
+ time_t oldEndTime = time(NULL);
+ time_t oldRunTime = oldEndTime - oldStartTime;
+ struct tm *oldRunTimeInfo = gmtime(&oldRunTime);
+ memset(timeBuf, 0, 100);
+ strftime(timeBuf, 100, "%X", oldRunTimeInfo);
+ fprintf(_fpReportFile, "\tDone. Elaspsed time for old version was %s.\n", timeBuf);
+
+ endMemoryProfile();
+
+ calcMemoryStats();
+
+
+
+ //run and time new version
+ fprintf(_fpReportFile, "\n\tRunning second command...\n");
+
+ startMemoryProfile(cmd2IsBedops);
+
+ time_t newStartTime = time(NULL);
+ int ret2 = system(cmd2.c_str());
+ if (ret2 !=0) {
+ fprintf(stderr, "\nError: received non-zero exit code %d from new version.\n", ret2);
+ return false;
+ }
+ time_t newEndTime = time(NULL);
+ time_t newRunTime = newEndTime - newStartTime;
+ struct tm *newRunTimeInfo = gmtime(&newRunTime);
+ memset(timeBuf, 0, 100);
+ strftime(timeBuf, 100, "%X", newRunTimeInfo);
+ fprintf(_fpReportFile, "\tDone. Elaspsed time for new version was %s.\n", timeBuf);
+
+ endMemoryProfile();
+
+ calcMemoryStats();
+
+ if (newRunTime < oldRunTime) { //new version is faster
+ time_t diffTime = oldRunTime - newRunTime;
+ struct tm *diffRunTimeInfo = gmtime(&diffTime);
+ memset(timeBuf, 0, 100);
+ strftime(timeBuf, 100, "%X", diffRunTimeInfo);
+
+ fprintf(_fpReportFile, "\n\tPASSED. New version is faster by %s", timeBuf);
+
+ if (newRunTime > 0) {
+ fprintf(_fpReportFile, ", or %7.2fx faster\n", (float)oldRunTime/(float)newRunTime);
+ } else {
+ fprintf(_fpReportFile, ", or ...WAY FASTER.\n");
+ }
+
+ } else if (oldRunTime < newRunTime) { //old version is faster
+ time_t diffTime = newRunTime - oldRunTime;
+ struct tm *diffRunTimeInfo = gmtime(&diffTime);
+
+ memset(timeBuf, 0, 100);
+ strftime(timeBuf, 100, "%X", diffRunTimeInfo);
+ fprintf(_fpReportFile, "\n\tFAILED. old version is faster by %s", timeBuf);
+
+ if (oldRunTime > 0) {
+ fprintf(_fpReportFile, ", or %7.2fx faster\n", (float)newRunTime/(float)oldRunTime);
+ } else {
+ fprintf(_fpReportFile, ", or ...WAY FASTER.\n");
+ }
+
+ } else { //run times were same.
+ fprintf(_fpReportFile, "\n\tMEH. No difference in speed.\n");
+ }
+
+ return true;
+}
+
+
+bool RegressTest::startMemoryProfile(bool isBedops)
+{
+ //kick off ps as a background process to monitor memory usage
+ string pidFilename = _tmpDirname + "pidFile.txt";
+ string psCmd;
+ if (!isBedops) {
+ psCmd = "while [ 1 ] ; do ps au | grep bedtools | grep ";
+ } else {
+ psCmd = "while [ 1 ] ; do ps au | grep bedops | grep ";
+ }
+ psCmd += _userName;
+ psCmd += " | grep -v grep | grep -v regresstest | grep -v \"sh -c\" >> ";
+ psCmd += _memoryLogfilename;
+ psCmd += " ; sleep .5 ; done & echo $! > ";
+ psCmd += _tmpDirname + "pidFile.txt";
+
+ if (system(psCmd.c_str()) != 0) {
+ fprintf(stderr, "Error: unable to launch top as background process for memory profiling.\n");
+ return false;
+ }
+
+ // open and parse the pidFile to get the process id of the memory profiling background process.
+ FILE *fp = fopen(pidFilename.c_str(), "r");
+ char sLine[4192];
+ memset(sLine, 0, 4192);
+ fgets(sLine, 4192, fp);
+ fclose(fp);
+
+ _currPidOfMemoryLogging = sLine;
+ return true;
+}
+
+bool RegressTest::endMemoryProfile()
+{
+
+ string killCmd = "kill -9 ";
+ killCmd += _currPidOfMemoryLogging;
+ if (system(killCmd.c_str()) != 0) {
+ fprintf(stderr, "Error: failed to kill process id %s\n", _currPidOfMemoryLogging.c_str());
+ return false;
+ }
+
+ return true;
+}
+
+bool RegressTest::calcMemoryStats()
+{
+ //read and parse the memory log file, calc basic stats: max, mean, median.
+ FILE *fp = fopen(_memoryLogfilename.c_str(), "r");
+ if (fp == NULL) {
+ fprintf(stderr, "Error: Unable to read memory profile log %s.\n", _memoryLogfilename.c_str());
+ return false;
+ }
+
+ char sLine[4192];
+ int numValidLines=0;
+ char field1[2048];
+ char field2[2048];
+ char field3[2048];
+ char field4[2048];
+ char field5[2048];
+
+ int totalMem= 0;
+ int currMem = 0;
+ int maxMem = 0;
+ while(!feof(fp)) {
+ memset(sLine, 0, 4192);
+ memset(field1, 0, 2048);
+ memset(field2, 0, 2048);
+ memset(field3, 0, 2048);
+ memset(field4, 0, 2048);
+ memset(field5, 0, 2048);
+
+ currMem = 0;
+ fgets(sLine, 4192, fp);
+ int len = strlen(sLine);
+ bool isValidLine = false;
+ for (int i=0; i < len; i++) {
+ if (!isspace(sLine[i])) {
+ isValidLine = true;
+ break;
+ }
+ }
+ if (isValidLine) {
+ numValidLines++;
+ sscanf(sLine, "%s %s %s %s %s", field1, field2, field3, field4, field5);
+
+ //now field 5 has the number of kilobytes the process used at that moment.
+ currMem = atoi(field5);
+ if (currMem == 0) {
+ //atoi failed. something wrong with input
+ fprintf(stderr, "Error: bad field where memory usage expected: %s.\n", field5);
+ fclose(fp);
+ return false;
+ }
+ maxMem = max(currMem, maxMem);
+ totalMem += currMem;
+ }
+ }
+
+ int avgMem = numValidLines > 0 ? totalMem / numValidLines : -1;
+
+ fclose(fp);
+ if (avgMem > 0) {
+ fprintf(_fpReportFile, "\tMemory uage: max = %dkb\tavg = %dkb\n", maxMem, avgMem);
+ } else {
+ fprintf(_fpReportFile, "\tMemory usage: TOO FAST TO PROFILE!\n");
+ }
+
+ //cleanup: erase memoryLogfile, as we wish to append to a blank file when next used.
+ if (remove(_memoryLogfilename.c_str()) != 0) {
+ fprintf(stderr, "Error: couldn't delete old memory logfile %s.\n", _memoryLogfilename.c_str());
+ return false;
+ }
+
+ return true;
+}
diff --git a/src/regressTest/RegressTest.h b/src/regressTest/RegressTest.h
new file mode 100644
index 0000000..93064dc
--- /dev/null
+++ b/src/regressTest/RegressTest.h
@@ -0,0 +1,93 @@
+/*
+ * RegressTest.h
+ *
+ * Created on: Dec 21, 2012
+ * Author: nek3d
+ */
+
+#ifndef REGRESSTEST_H_
+#define REGRESSTEST_H_
+
+using namespace std;
+
+#include <string>
+#include <cstdio>
+#include <vector>
+#include <fstream>
+class SingleLineDelimTextFileReader;
+class BufferedStreamMgr;
+
+class RegressTest {
+public:
+ RegressTest();
+ ~RegressTest();
+ bool init(int argc, char **argv);
+
+ void setFilesPerRun(int numFiles) { _filesPerRun = numFiles; }
+ void addFilePrecessorOption(const char *option) { _filePrecessorOptions.push_back(option); }
+ bool runTests();
+
+
+
+protected:
+ string _configFilename;
+ string _newVersion;
+ string _subProgram;
+ string _oldVersion;
+
+ string _hardOptions;
+ vector<string> _softOptions;
+
+ int _filesPerRun;
+ vector<string> _filePrecessorOptions;
+
+ FILE *_fpReportFile;
+ ifstream _configFile;
+
+ typedef vector<pair<string, string> > fileListType;
+ fileListType *_correctFiles; //list of files for correctness tests. First in pair is file name, second is description.
+ fileListType *_performFiles; //list of files for performance tests. First in pair is file name, second is description.
+
+ //config file key words
+ static const string _hardOptsCmd;
+ static const string _correctCmd;
+ static const string _performCmd;
+ static const string _randomCmd;
+
+ //useful strings to have for building command strings
+ static const string _space;
+ static const string _redirect;
+ static const string _devNull;
+ static const string _bedOpsCmd;
+
+ int _generatedFileNumber; // a "tag" to give generatedFiles.
+
+ string _tmpDirname;
+ string _memoryLogfilename;
+ string _currPidOfMemoryLogging;
+ string _userName;
+
+ //Special: Since RegressTest was originally designed only for testing bedtools against prior versions
+ // of itself, some hacking is needed to make it play with bedops.
+ bool _isOldProgBedops;
+
+
+ bool parseParams(int argc, char **argv);
+ void usage() const;
+ void echoOptions() const;
+ bool config();
+ bool parseConfigLines(int numLinesToRead, bool correctnessFiles);
+ bool generateRandomFile(const string & randomArgs, string &filename);
+
+ bool performTests(bool correctness); //pass true for correctness, false for performance.
+ bool executeAndCompareCorrectness(const fileListType &cmdAndOutput);
+ bool executeAndComparePerformance(const fileListType &cmdAndOutput);
+
+ bool startMemoryProfile(bool isBedops);
+ bool endMemoryProfile();
+ bool calcMemoryStats();
+
+};
+
+
+#endif /* REGRESSTEST_H_ */
diff --git a/src/regressTest/regressTestMain.cpp b/src/regressTest/regressTestMain.cpp
new file mode 100644
index 0000000..0377ca6
--- /dev/null
+++ b/src/regressTest/regressTestMain.cpp
@@ -0,0 +1,67 @@
+
+#include "RegressTest.h"
+#include <cstring>
+#include <cstdlib>
+#include <cstdio>
+#include "QuickString.h"
+
+void usage() {
+ printf("Usage: bedtools regressTest sub-prog targetVersion configFile [optionsToTest]\n");
+}
+
+void setOneWayOptions(RegressTest *regressTest) {
+ //Use this for programs whose main arguments are two files, preceded by -a and -b, respectively.
+
+ regressTest->setFilesPerRun(1);
+ regressTest->addFilePrecessorOption("-i");
+}
+
+void setTwoWayOptions(RegressTest *regressTest) {
+ //Use this for programs whose main arguments are two files, preceded by -a and -b, respectively.
+
+ regressTest->setFilesPerRun(2);
+ regressTest->addFilePrecessorOption("-a");
+ regressTest->addFilePrecessorOption("-b");
+}
+
+int regress_test_main(int argc, char **argv) {
+
+ //usage: bedtools regressTest sub-prog targetVersion [optionsToTest]
+ if (argc < 5) {
+ usage();
+ exit(1);
+ }
+ QuickString program(argv[2]);
+
+ RegressTest *regressTest = new RegressTest();
+
+ //set specific options for each sub-program
+ if (program == "intersect") {
+ setTwoWayOptions(regressTest);
+ } else if (program == "jaccard") {
+ setTwoWayOptions(regressTest);
+ } else if (program == "merge") {
+ setOneWayOptions(regressTest);
+ } else {
+ //TBD: Handle all other programs eventually
+ fprintf(stderr, "Sorry, sub-program %s is not yet supported.\n", argv[2]);
+ delete regressTest;
+ exit(1);
+ }
+
+ if (!regressTest->init(argc, argv)) {
+ fprintf(stderr, "Error: could not initialize tests for %s.\n", argv[2]);
+ delete regressTest;
+ exit(1);
+ }
+
+ if (!regressTest->runTests()) {
+ fprintf(stderr, "Error: Failed to run tests for %s.\n", argv[2]);
+ delete regressTest;
+ exit(1);
+ }
+
+ delete regressTest;
+ exit(0);
+
+}
diff --git a/src/intersectBed/Makefile b/src/reldist/Makefile
similarity index 84%
copy from src/intersectBed/Makefile
copy to src/reldist/Makefile
index 33fc091..6b7f941 100644
--- a/src/intersectBed/Makefile
+++ b/src/reldist/Makefile
@@ -19,10 +19,10 @@ INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= intersectMain.cpp intersectBed.cpp intersectBed.h
-OBJECTS= intersectMain.o intersectBed.o
+SOURCES= reldistMain.cpp reldist.cpp reldist.h
+OBJECTS= reldistMain.o reldist.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= intersectBed
+PROGRAM= reldist
all: $(BUILT_OBJECTS)
@@ -34,6 +34,6 @@ $(BUILT_OBJECTS): $(SOURCES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectBed.o
+ @rm -f $(OBJ_DIR)/reldistMain.o $(OBJ_DIR)/reldist.o
.PHONY: clean
diff --git a/src/reldist/reldist.cpp b/src/reldist/reldist.cpp
new file mode 100644
index 0000000..699d857
--- /dev/null
+++ b/src/reldist/reldist.cpp
@@ -0,0 +1,154 @@
+/*****************************************************************************
+ reldist.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "lineFileUtilities.h"
+#include "reldist.h"
+
+/*
+ Constructor
+*/
+RelativeDistance::RelativeDistance(string bedAFile,
+ string bedBFile,
+ bool summary)
+{
+ _bedAFile = bedAFile;
+ _bedBFile = bedBFile;
+ _summary = summary;
+ _tot_queries = 0;
+ CalculateRelativeDistance();
+}
+
+
+/*
+ Destructor
+*/
+RelativeDistance::~RelativeDistance(void) {
+}
+
+
+void RelativeDistance::LoadMidpoints() {
+
+ _bedB = new BedFile(_bedBFile);
+
+ BED bed;
+ _bedB->Open();
+ while (_bedB->GetNextBed(bed)) {
+ CHRPOS midpoint = (int) (bed.end + bed.start) / 2;
+ _db_midpoints[bed.chrom].push_back(midpoint);
+ }
+
+ map<string, vector<CHRPOS> >::const_iterator midItr = _db_midpoints.begin();
+ map<string, vector<CHRPOS> >::const_iterator midEnd = _db_midpoints.end();
+ for (; midItr != midEnd; ++midItr)
+ {
+ sort(_db_midpoints[midItr->first].begin(),
+ _db_midpoints[midItr->first].end());
+ }
+}
+
+
+void RelativeDistance::ReportDistanceSummary()
+{
+ cout << "reldist\t"
+ << "count\t"
+ << "total\t"
+ << "fraction\n";
+
+ map<float, size_t>::const_iterator freqItr = _reldists.begin();
+ map<float, size_t>::const_iterator freqEnd = _reldists.end();
+ for (; freqItr != freqEnd; ++freqItr)
+ {
+ printf("%.2f\t%lu\t%lu\t%.3f\n",
+ freqItr->first,
+ freqItr->second,
+ _tot_queries,
+ (float) freqItr->second / (float) _tot_queries);
+ }
+}
+
+
+void RelativeDistance::UpdateDistanceSummary(float rel_dist)
+{
+ _tot_queries++;
+ // round the relative distance to two decimal places.
+ float rounded_rel_dist = floorf(rel_dist * 100) / 100;
+ _reldists[rounded_rel_dist]++;
+}
+
+
+void RelativeDistance::CalculateRelativeDistance()
+{
+ LoadMidpoints();
+
+ vector<CHRPOS>::iterator low;
+ size_t low_idx, high_idx;
+ float rel_dist;
+
+ _bedA = new BedFile(_bedAFile);
+
+ BED bed;
+ _bedA->Open();
+ while (_bedA->GetNextBed(bed)) {
+
+ if (_bedA->_status != BED_VALID)
+ continue;
+
+ vector<CHRPOS> *chrom_mids = &_db_midpoints[bed.chrom];
+ // binary search the current query's midpoint among
+ // the database midpoints
+ int midpoint = (int) (bed.end + bed.start) / 2;
+ low = lower_bound(chrom_mids->begin(),
+ chrom_mids->end(),
+ midpoint);
+
+ // grab the indicies for the database midpoints that are left and
+ // right of the query's midpoint.
+ low_idx = low - chrom_mids->begin() - 1;
+ high_idx = low_idx + 1;
+
+ // make sure we don't run off the boundaries of the database's
+ // midpoint vector
+ if (low_idx != chrom_mids->size() - 1)
+ {
+ // grab the database midpoints that are left and right of
+ // the query's midpoint.
+ int left = (*chrom_mids)[low_idx];
+ int right = (*chrom_mids)[high_idx];
+
+ // ?
+ if (left > midpoint)
+ continue;
+
+ // calculate the relative distance between the query's midpoint
+ // and the two nearest database midpoints.
+ size_t left_dist = abs(midpoint-left);
+ size_t right_dist = abs(midpoint-right);
+ rel_dist = (float) min(left_dist, right_dist)
+ /
+ (float) (right-left);
+
+ if (!_summary)
+ {
+ _bedA->reportBedTab(bed);
+ printf("%.3f\n", rel_dist);
+ }
+ else {
+ UpdateDistanceSummary(rel_dist);
+ }
+ }
+ }
+
+ // report the "histogram" of distances.
+ if (_summary)
+ ReportDistanceSummary();
+}
+
+
diff --git a/src/jaccard/jaccard.h b/src/reldist/reldist.h
similarity index 66%
copy from src/jaccard/jaccard.h
copy to src/reldist/reldist.h
index f0e3fd7..a1ea421 100644
--- a/src/jaccard/jaccard.h
+++ b/src/reldist/reldist.h
@@ -1,5 +1,5 @@
/*****************************************************************************
- jaccard.h
+ reldist.h
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -9,8 +9,8 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#ifndef JACCARD_H
-#define JACCARD_H
+#ifndef RELDIST_H
+#define RELDIST_H
#include "bedFile.h"
#include "chromsweep.h"
@@ -22,23 +22,26 @@ using namespace BamTools;
#include <vector>
+#include <algorithm>
#include <iostream>
#include <fstream>
#include <stdlib.h>
+#include <math.h>
using namespace std;
-class Jaccard {
+class RelativeDistance {
public:
// constructor
- Jaccard(string bedAFile, string bedBFile,
- float overlapFraction, bool reciprocal);
+ RelativeDistance(string bedAFile,
+ string bedBFile,
+ bool _summary);
// destructor
- ~Jaccard(void);
+ ~RelativeDistance(void);
private:
@@ -47,22 +50,25 @@ private:
//------------------------------------------------
string _bedAFile;
string _bedBFile;
-
- bool _reciprocal;
- float _overlapFraction;
-
+
+ map<string, vector<CHRPOS> > _db_midpoints;
+ map<float, size_t> _reldists;
+ size_t _tot_queries;
+
// instance of a bed file class.
BedFile *_bedA, *_bedB;
+ bool _summary;
//------------------------------------------------
// private methods
//------------------------------------------------
- unsigned long GetIntersection();
- unsigned long GetUnion();
- void CalculateJaccard();
+ void LoadMidpoints();
+ void CalculateRelativeDistance();
+ void UpdateDistanceSummary(float rel_dist);
+ void ReportDistanceSummary();
+
- size_t GetTotalIntersection(const BED &a, const vector<BED> &hits);
};
-#endif /* JACCARD_H */
+#endif /* RELDIST_H */
diff --git a/src/jaccard/jaccardMain.cpp b/src/reldist/reldistMain.cpp
similarity index 51%
copy from src/jaccard/jaccardMain.cpp
copy to src/reldist/reldistMain.cpp
index cc175d1..82a178a 100644
--- a/src/jaccard/jaccardMain.cpp
+++ b/src/reldist/reldistMain.cpp
@@ -1,5 +1,5 @@
/*****************************************************************************
- jaccardMain.cpp
+ reldistMain.cpp
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -9,22 +9,22 @@
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "jaccard.h"
+#include "reldist.h"
#include "version.h"
using namespace std;
// define our program name
-#define PROGRAM_NAME "bedtools jaccard"
+#define PROGRAM_NAME "bedtools reldist"
// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
// function declarations
-void jaccard_help(void);
+void reldist_help(void);
-int jaccard_main(int argc, char* argv[]) {
+int reldist_main(int argc, char* argv[]) {
// our configuration variables
bool showHelp = false;
@@ -32,14 +32,11 @@ int jaccard_main(int argc, char* argv[]) {
// input files
string bedAFile;
string bedBFile;
+ bool summary = true;
// input arguments
- float overlapFraction = 1E-9;
-
bool haveBedA = false;
bool haveBedB = false;
- bool haveFraction = false;
- bool reciprocalFraction = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -53,7 +50,7 @@ int jaccard_main(int argc, char* argv[]) {
}
}
- if(showHelp) jaccard_help();
+ if(showHelp) reldist_help();
// do some parsing (all of these parameters require 2 strings)
for(int i = 1; i < argc; i++) {
@@ -74,15 +71,8 @@ int jaccard_main(int argc, char* argv[]) {
i++;
}
}
- else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
- if ((i+1) < argc) {
- haveFraction = true;
- overlapFraction = atof(argv[i + 1]);
- i++;
- }
- }
- else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
- reciprocalFraction = true;
+ else if(PARAMETER_CHECK("-detail", 7, parameterLength)) {
+ summary = false;
}
else {
cerr << endl
@@ -96,56 +86,50 @@ int jaccard_main(int argc, char* argv[]) {
// make sure we have both input files
if (!haveBedA || !haveBedB) {
- cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+ cerr << endl
+ << "*****"
+ << endl
+ << "*****ERROR: Need -a and -b files. "
+ << endl
+ << "*****"
+ << endl;
showHelp = true;
}
- if (reciprocalFraction && !haveFraction) {
- cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
- showHelp = true;
- }
if (!showHelp) {
- Jaccard *j = new Jaccard(bedAFile, bedBFile,
- overlapFraction, reciprocalFraction);
- delete j;
+ RelativeDistance *rd = new RelativeDistance(bedAFile,
+ bedBFile,
+ summary);
+ delete rd;
return 0;
}
else {
- jaccard_help();
+ reldist_help();
return 0;
}
}
-void jaccard_help(void) {
+void reldist_help(void) {
- cerr << "\nTool: bedtools jaccard (aka jaccard)" << endl;
+ cerr << "\nTool: bedtools reldist" << endl;
cerr << "Version: " << VERSION << "\n";
- cerr << "Summary: Calculate Jaccard statistic b/w two feature files."
- << endl
- << "\t Jaccard is the length of the intersection over the union."
- << endl
- << "\t Values range from 0 (no intersection) to 1 (self intersection)."
+ cerr << "Summary: Calculate the relative distance distribution "
+ << "b/w two feature files."
<< endl << endl;
- cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
+ cerr << "Usage: "
+ << PROGRAM_NAME
+ << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>"
+ << endl << endl;
cerr << "Options: " << endl;
- cerr << "\t-f\t" << "Minimum overlap required as a fraction of A." << endl;
- cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
- cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
-
- cerr << "\t-r\t" << "Require that the fraction overlap be reciprocal for A and B." << endl;
- cerr << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
- cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
-
- cerr << "Notes: " << endl;
- cerr << "\t(1) Input files must be sorted by chrom, then start position."
- << endl << endl;
-
+ cerr << "\t-detail\t" << "Instead of a summary, report the relative"
+ << "\t\t distance for each interval in A"
+ << endl << endl;
// end the program here
exit(1);
diff --git a/src/intersectBed/Makefile b/src/sampleFile/Makefile
similarity index 50%
rename from src/intersectBed/Makefile
rename to src/sampleFile/Makefile
index 33fc091..2042291 100644
--- a/src/intersectBed/Makefile
+++ b/src/sampleFile/Makefile
@@ -5,24 +5,28 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/gzstream/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
- -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
+INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src \
-I$(UTILITIES_DIR)/BlockedIntervals \
-I$(UTILITIES_DIR)/BamTools-Ancillary \
- -I$(UTILITIES_DIR)/chromsweep \
- -I$(UTILITIES_DIR)/version/
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
+ -I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= intersectMain.cpp intersectBed.cpp intersectBed.h
-OBJECTS= intersectMain.o intersectBed.o
+SOURCES= sampleMain.cpp SampleFile.cpp SampleFile.h
+OBJECTS= sampleMain.o SampleFile.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-PROGRAM= intersectBed
+PROGRAM= sample
all: $(BUILT_OBJECTS)
@@ -34,6 +38,6 @@ $(BUILT_OBJECTS): $(SOURCES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/intersectMain.o $(OBJ_DIR)/intersectBed.o
+ @rm -f $(OBJ_DIR)/sampleMain.o $(OBJ_DIR)/SampleFile.o
.PHONY: clean
diff --git a/src/sampleFile/SampleFile.cpp b/src/sampleFile/SampleFile.cpp
new file mode 100644
index 0000000..8291824
--- /dev/null
+++ b/src/sampleFile/SampleFile.cpp
@@ -0,0 +1,121 @@
+/*
+ * SampleFile.cpp
+ *
+ * Created on: Nov 18, 2013
+ * Author: nek3d
+ */
+
+#include "SampleFile.h"
+#include "ContextSample.h"
+#include "FileRecordMgr.h"
+#include "RecordOutputMgr.h"
+
+static const bool SampleRecordLtFn(const Record *rec1, const Record *rec2) {
+ return (*rec1 < *rec2);
+}
+
+SampleFile::SampleFile(ContextSample *context)
+: _context(context),
+ _inputFile(NULL),
+ _outputMgr(NULL),
+ _numSamples(0),
+ _numCurrSamples(0),
+ _currRecordNum(0)
+{
+ _numSamples = context->getNumOutputRecords();
+ if (_numSamples == 0) {
+ _numSamples = DEFAULT_NUM_SAMPLES;
+ }
+}
+
+SampleFile::~SampleFile() {
+
+}
+
+bool SampleFile::takeSample()
+{
+ //we're only operating on one file, so the idx is zero.
+ _inputFile = _context->getFile(0);
+ _samples.resize(_numSamples, NULL);
+
+
+ //Context object takes care of the seed, either user given or randomly
+ //generated, and seeds the call to srand with it, so we don't have to
+ //here.
+ if (!_context->hasConstantSeed()) {
+ _context->getUnspecifiedSeed();
+ }
+
+ _outputMgr = new RecordOutputMgr();
+ _outputMgr->init(_context);
+
+
+ while (!_inputFile->eof()) {
+ Record *record = _inputFile->allocateAndGetNextRecord();
+ if (record == NULL) {
+ continue;
+ }
+ if (!keepRecord(record)) {
+ _inputFile->deleteRecord(record);
+ }
+ _currRecordNum++;
+ }
+
+ if (_currRecordNum < _numSamples) {
+ //die with error;
+ cerr << "\n***** ERROR: Input file has fewer records than the requested number of output records. *****" << endl << endl;
+ exit(1);
+ }
+
+ //If the output type is BAM, must sort the output records.
+ if (_context->getOutputFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ sort(_samples.begin(), _samples.end(), SampleRecordLtFn);
+ }
+ // Now output all the kept records, then do cleanup.
+ for (size_t i=0; i < _numSamples; i++) {
+ _outputMgr->printRecord(_samples[i]);
+ }
+ delete _outputMgr;
+ _inputFile->close();
+ return true;
+}
+
+bool SampleFile::keepRecord(Record *record)
+{
+ if (!strandComplies(record)) {
+ return false;
+ }
+ if (_numCurrSamples < _numSamples) {
+ _samples[_numCurrSamples] = record;
+ _numCurrSamples++;
+ return true;
+ }
+
+
+ // We need a random number in the range [0, _currRecordNum].
+ // Must combine two consective calls to rand()
+ // because RAND_MAX is 2^31 (2147483648), whereas
+ // the number of input records could be far larger.
+ size_t idx = ((((long) rand()) << 31) | rand()) % _currRecordNum;
+
+ if (idx < _numSamples) {
+ //replace old record at idx with this new one.
+ _inputFile->deleteRecord(_samples[idx]);
+ _samples[idx] = record;
+ return true;
+ }
+ return false;
+}
+
+bool SampleFile::strandComplies(const Record * record) {
+ if (!_context->getSameStrand()) {
+ return true;
+ }
+ if (_context->getForwardOnly() && record->getStrandVal() == Record::FORWARD) {
+ return true;
+ }
+ if (_context->getReverseOnly() && record->getStrandVal() == Record::REVERSE) {
+ return true;
+ }
+ return false;
+}
diff --git a/src/sampleFile/SampleFile.h b/src/sampleFile/SampleFile.h
new file mode 100644
index 0000000..11a1b49
--- /dev/null
+++ b/src/sampleFile/SampleFile.h
@@ -0,0 +1,43 @@
+/*
+ * SampleFile.h
+ *
+ * Created on: Nov 18, 2013
+ * Author: nek3d
+ */
+
+#ifndef SAMPLEFILE_H_
+#define SAMPLEFILE_H_
+
+using namespace std;
+
+#include "ContextSample.h"
+#include "Record.h"
+#include <vector>
+
+class FileRecordMgr;
+class Context;
+class RecordOutputMgr;
+
+class SampleFile {
+public:
+ SampleFile(ContextSample *context);
+ ~SampleFile();
+ bool takeSample();
+
+private:
+ ContextSample *_context;
+ FileRecordMgr *_inputFile;
+ RecordOutputMgr *_outputMgr;
+ vector<Record *> _samples;
+ size_t _numSamples; //the number of samples we ultimately want
+ size_t _numCurrSamples; //the number of samples kept so far.
+ size_t _currRecordNum;
+ int _seed;
+
+ static const int DEFAULT_NUM_SAMPLES = 1000000;
+ bool keepRecord(Record *record);
+ bool strandComplies(const Record * record);
+
+};
+
+#endif /* SAMPLEFILE_H_ */
diff --git a/src/sampleFile/sampleMain.cpp b/src/sampleFile/sampleMain.cpp
new file mode 100644
index 0000000..2fe1742
--- /dev/null
+++ b/src/sampleFile/sampleMain.cpp
@@ -0,0 +1,77 @@
+/*
+ * sampleMain.cpp
+ *
+ * Created on: Nov 18, 2013
+ * Author: nek3d
+ */
+
+#include <iostream>
+#include "ContextSample.h"
+#include "SampleFile.h"
+
+#define PROGRAM_NAME "bedtools sample"
+
+void sample_help(void);
+
+int sample_main(int argc, char **argv)
+{
+ ContextSample *context = new ContextSample();
+ if (!context->parseCmdArgs(argc, argv, 1) || context->getShowHelp() || !context->isValidState()) {
+ if (!context->getErrorMsg().empty()) {
+ cerr << context->getErrorMsg() << endl;
+ }
+ sample_help();
+ delete context;
+ return 0;
+ }
+ SampleFile *sampleFile = new SampleFile(context);
+
+ bool retVal = sampleFile->takeSample();
+ delete sampleFile;
+ delete context;
+ return retVal ? 0 : 1;
+
+}
+
+void sample_help(void) {
+
+ cerr << "\nTool: bedtools sample (aka sampleFile)" << endl;
+ cerr << "Version: " << VERSION << "\n";
+ cerr << "Summary: Take sample of input file(s) using reservoir sampling algorithm." << endl << endl;
+
+ cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf/bam>" << endl << endl;
+
+ cerr << "WARNING:\tThe current sample algorithm will hold all requested sample records in memory prior to output." << endl;
+ cerr << "\t\tThe user must ensure that there is adequate memory for this." << endl << endl;
+ cerr << "Options: " << endl;
+
+ cerr << "\t-n\t" << "The number of records to generate." << endl;
+ cerr << "\t\t- Default = 1,000,000." << endl;
+ cerr << "\t\t- (INTEGER)" << endl << endl;
+
+ cerr << "\t-seed\t" << "Supply an integer seed for the shuffling." << endl;
+ cerr << "\t\t- By default, the seed is chosen automatically." << endl;
+ cerr << "\t\t- (INTEGER)" << endl << endl;
+
+
+ cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
+
+ cerr << "\t-bed\t" << "When using BAM input (-abam), write output as BED. The default" << endl;
+ cerr << "\t\tis to write output in BAM when using -abam." << endl << endl;
+
+ cerr << "\t-s\t" << "Require same strandedness. That is, only give records" << endl;
+ cerr << "\t\tthat have the same strand. Use '-s forward' or '-s reverse'" << endl;
+ cerr << "\t\tfor forward or reverse strand records, respectively." << endl;
+ cerr << "\t\t- By default, records are reported without respect to strand." << endl << endl;
+
+ cerr << "\t-header\t" << "Print the header from the input file prior to results." << endl << endl;
+
+ cerr << "Notes: " << endl;
+ cerr << "\tTBD: Enter other usage notes here." << endl << endl;
+
+ // end the program here
+ exit(1);
+
+}
+
+
diff --git a/src/shuffleBed/Makefile b/src/shuffleBed/Makefile
index 2f94571..a85f2df 100644
--- a/src/shuffleBed/Makefile
+++ b/src/shuffleBed/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/bedFilePE/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index 8a30749..518e237 100644
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -18,7 +18,9 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
bool haveSeed, bool haveExclude,
bool haveInclude, bool sameChrom,
float overlapFraction, int seed,
- bool chooseChrom, bool isBedpe) {
+ bool chooseChrom, bool isBedpe, size_t maxTries,
+ bool noOverlapping, bool preventExceedingChromEnd)
+{
_bedFile = bedFile;
_genomeFile = genomeFile;
@@ -31,6 +33,9 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
_haveSeed = haveSeed;
_chooseChrom = chooseChrom;
_isBedpe = isBedpe;
+ _maxTries = maxTries;
+ _noOverlapping = noOverlapping;
+ _preventExceedingChromEnd = preventExceedingChromEnd;
// use the supplied seed for the random
@@ -60,13 +65,19 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
_exclude = new BedFile(excludeFile);
_exclude->loadBedFileIntoMap();
}
+ else if (_noOverlapping) {
+ // create an empty map that we add to as we iterate.
+ _exclude = new BedFile();
+ // force down correct code-path.
+ _haveExclude = true;
+ }
if (_haveInclude) {
_include = new BedFile(includeFile);
_include->loadBedFileIntoMapNoBin();
_numIncludeChroms = 0;
- masterBedMapNoBin::const_iterator it = _include->bedMapNoBin.begin();
+ masterBedMapNoBin::const_iterator it = _include->bedMapNoBin.begin();
masterBedMapNoBin::const_iterator itEnd = _include->bedMapNoBin.end();
for(; it != itEnd; ++it) {
_includeChroms.push_back(it->first);
@@ -78,6 +89,8 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
ShuffleWithExclusions();
else if (_haveExclude == false && _haveInclude == true)
ShuffleWithInclusions();
+ else if (_haveExclude == true && _haveInclude == true)
+ ShuffleWithInclusionsAndExclusions();
else
Shuffle();
}
@@ -96,6 +109,9 @@ void BedShuffle::Shuffle() {
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
ChooseLocus(bedEntry);
+ if(_noOverlapping){
+ _exclude->addBEDIntoMap(bedEntry);
+ }
_bed->reportBedNewLine(bedEntry);
}
}
@@ -108,7 +124,8 @@ void BedShuffle::Shuffle() {
BEDPE bedEntry, nullBedPE;
_bedpe->Open();
- while ((status = _bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
+ while ((status =
+ _bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
{
if (status == BED_VALID) {
ChoosePairedLocus(bedEntry);
@@ -132,7 +149,7 @@ void BedShuffle::ShuffleWithExclusions() {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
- int tries = 0;
+ size_t tries = 0;
bool haveOverlap = false;
do
{
@@ -145,16 +162,20 @@ void BedShuffle::ShuffleWithExclusions() {
false, false,
_overlapFraction, false);
tries++;
- } while ((haveOverlap == true) && (tries <= MAX_TRIES));
-
+ } while ((haveOverlap == true) && (tries <= _maxTries));
- if (tries > MAX_TRIES) {
+
+ if (tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
- << ": tried " << MAX_TRIES
+ << ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl; }
else {
+ if(_noOverlapping){
+ // future entries cannot overlap this one
+ _exclude->addBEDIntoMap(bedEntry);
+ }
_bed->reportBedNewLine(bedEntry);
}
}
@@ -168,13 +189,14 @@ void BedShuffle::ShuffleWithExclusions() {
BEDPE bedEntry;
_bedpe->Open();
- while ((status = _bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
+ while ((status =
+ _bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
{
if (status == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
- int tries = 0;
+ size_t tries = 0;
bool haveOverlap1 = false;
bool haveOverlap2 = false;
do
@@ -196,11 +218,11 @@ void BedShuffle::ShuffleWithExclusions() {
_overlapFraction, false);
tries++;
} while (((haveOverlap1 == true) || (haveOverlap2 == true))
- && (tries <= MAX_TRIES));
+ && (tries <= _maxTries));
- if (tries > MAX_TRIES) {
+ if (tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
- << ": tried " << MAX_TRIES
+ << ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl;
@@ -219,19 +241,78 @@ void BedShuffle::ShuffleWithExclusions() {
void BedShuffle::ShuffleWithInclusions() {
BED bedEntry; // used to store the current BED line from the BED file.
-
+ CHRPOS chromSize;
+
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
+ size_t tries = 0;
// choose a new locus
- ChooseLocusFromInclusionFile(bedEntry);
- _bed->reportBedNewLine(bedEntry);
+ do {
+ ChooseLocusFromInclusionFile(bedEntry);
+ chromSize = _genome->getChromSize(bedEntry.chrom);
+ tries++;
+ } while ((bedEntry.end > chromSize)
+ && (tries <= _maxTries));
+ if (tries > _maxTries) {
+ cerr << "Error, line " << _bed->_lineNum
+ << ": tried " << _maxTries
+ << " potential loci for entry, but could not avoid "
+ << "excluded regions. Ignoring entry and moving on."
+ << endl; }
+ else {
+ _bed->reportBedNewLine(bedEntry);
+ }
}
}
_bed->Close();
}
+void BedShuffle::ShuffleWithInclusionsAndExclusions() {
+
+ BED bedEntry; // used to store the current BED line from the BED file.
+
+ _bed->Open();
+ while (_bed->GetNextBed(bedEntry)) {
+ if (_bed->_status == BED_VALID) {
+
+ // keep looking as long as the chosen
+ // locus happens to overlap with regions
+ // that the user wishes to exclude.
+ size_t tries = 0;
+ bool haveOverlap = false;
+ do
+ {
+ // choose a new locus
+ ChooseLocusFromInclusionFile(bedEntry);
+ haveOverlap = _exclude->anyHits(bedEntry.chrom,
+ bedEntry.start,
+ bedEntry.end,
+ bedEntry.strand,
+ false, false,
+ _overlapFraction, false);
+ tries++;
+ } while ((haveOverlap == true) && (tries <= _maxTries));
+
+
+ if (tries > _maxTries) {
+ cerr << "Error, line " << _bed->_lineNum
+ << ": tried " << _maxTries
+ << " potential loci for entry, but could not avoid "
+ << "excluded regions. Ignoring entry and moving on."
+ << endl; }
+ else {
+ _bed->reportBedNewLine(bedEntry);
+ if (_noOverlapping){
+ _exclude->addBEDIntoMap(bedEntry);
+ }
+ }
+ }
+ }
+ _bed->Close();
+}
+
void BedShuffle::ChooseLocus(BED &bedEntry) {
string randomChrom;
@@ -250,7 +331,8 @@ void BedShuffle::ChooseLocus(BED &bedEntry) {
// we need to combine two consective calls to rand()
// because RAND_MAX is 2^31 (2147483648), whereas
// mammalian genomes are obviously much larger.
- uint32_t randStart = ((((long) rand()) << 31) | rand()) % _genomeSize;
+ uint32_t randStart = ((((long) rand()) << 31) | rand()) %
+ _genomeSize;
// use the above randomStart (e.g., for human 0..3.1billion)
// to identify the chrom and start on that chrom.
pair<string, int> location = _genome->projectOnGenome(randStart);
@@ -258,6 +340,14 @@ void BedShuffle::ChooseLocus(BED &bedEntry) {
bedEntry.start = location.second;
bedEntry.end = bedEntry.start + length;
chromSize = _genome->getChromSize(location.first);
+
+ if ((bedEntry.end > chromSize) &&
+ (_preventExceedingChromEnd == false))
+ {
+ bedEntry.end = chromSize;
+ break;
+ }
+
} while (bedEntry.end > chromSize);
// keep looking if we have exceeded the end of the chrom.
}
@@ -282,6 +372,14 @@ void BedShuffle::ChooseLocus(BED &bedEntry) {
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
}
+
+ if ((bedEntry.end > chromSize) &&
+ (_preventExceedingChromEnd == false))
+ {
+ bedEntry.end = chromSize;
+ break;
+ }
+
} while (bedEntry.end > chromSize);
}
}
@@ -298,7 +396,8 @@ void BedShuffle::ChoosePairedLocus(BEDPE &b) {
CHRPOS chromSize;
do
{
- uint32_t randStart = ((((long) rand()) << 31) | rand()) % _genomeSize;
+ uint32_t randStart = ((((long) rand()) << 31) | rand()) %
+ _genomeSize;
pair<string, int> location = _genome->projectOnGenome(randStart);
b.chrom1 = location.first;
b.chrom2 = location.first;
@@ -317,8 +416,10 @@ void BedShuffle::ChoosePairedLocus(BEDPE &b) {
CHRPOS chromSize1, chromSize2;
do
{
- uint32_t rand1Start = ((((long) rand()) << 31) | rand()) % _genomeSize;
- uint32_t rand2Start = ((((long) rand()) << 31) | rand()) % _genomeSize;
+ uint32_t rand1Start = ((((long) rand()) << 31) | rand()) %
+ _genomeSize;
+ uint32_t rand2Start = ((((long) rand()) << 31) | rand()) %
+ _genomeSize;
pair<string, int> location1 = _genome->projectOnGenome(rand1Start);
pair<string, int> location2 = _genome->projectOnGenome(rand2Start);
@@ -362,20 +463,22 @@ void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry) {
bedEntry.chrom = randomChrom;
}
else {
- // get the number of inclusion intervals for the original chrom
- size_t size = _include->bedMapNoBin[chrom].size();
- // grab a random interval on the chosen chromosome.
- includeInterval = _include->bedMapNoBin[chrom][rand() % size];
+ if ( _include->bedMapNoBin.find(chrom) != _include->bedMapNoBin.end() )
+ {
+ // get the number of inclusion intervals for the original chrom
+ size_t size = _include->bedMapNoBin[chrom].size();
+ // grab a random interval on the chosen chromosome.
+ includeInterval = _include->bedMapNoBin[chrom][rand() % size];
+ }
+ else {
+ cerr << "Error, line " << _bed->_lineNum
+ << ": the requested chromosome ("
+ << chrom
+ << ") cannot "
+ << "be found in the -incl file " << endl;
+ }
}
-
randomStart = includeInterval.start + rand() % (includeInterval.size());
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
-
- // use recursion to ensure that the chosen location
- // doesn't go past the end of the chrom
- if (bedEntry.end > ((size_t) _genome->getChromSize(chrom))) {
- //bedEntry.end = _genome->getChromSize(chrom);
- ChooseLocusFromInclusionFile(bedEntry);
- }
}
diff --git a/src/shuffleBed/shuffleBed.h b/src/shuffleBed/shuffleBed.h
index 648a34d..5bfe74e 100644
--- a/src/shuffleBed/shuffleBed.h
+++ b/src/shuffleBed/shuffleBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
#include "bedFilePE.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
@@ -25,8 +25,6 @@
#include <algorithm> // for binary search
using namespace std;
-const int MAX_TRIES = 1000000;
-
//************************************************
// Class methods and elements
//************************************************
@@ -40,7 +38,9 @@ public:
bool haveSeed, bool haveExclude,
bool haveInclude, bool sameChrom,
float overlapFraction, int seed,
- bool chooseChrom, bool isBedpe);
+ bool chooseChrom, bool isBedpe,
+ size_t _maxTries, bool noOverlapping,
+ bool preventExceedingChromEnd);
// destructor
~BedShuffle(void);
@@ -59,6 +59,9 @@ private:
bool _haveSeed;
bool _chooseChrom;
bool _isBedpe;
+ size_t _maxTries;
+ bool _noOverlapping;
+ bool _preventExceedingChromEnd;
// The BED file from which to compute coverage.
@@ -79,6 +82,7 @@ private:
void Shuffle();
void ShuffleWithExclusions();
void ShuffleWithInclusions();
+ void ShuffleWithInclusionsAndExclusions();
void ChooseLocus(BED &);
void ChooseLocusFromInclusionFile(BED &);
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index 8edb6a4..c53dad5 100644
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -40,11 +40,14 @@ int shuffle_main(int argc, char* argv[]) {
bool haveExclude = false;
bool haveInclude = false;
bool haveSeed = false;
- float overlapFraction = 0.0;
+ float overlapFraction = 1E-9;
int seed = -1;
bool sameChrom = false;
bool chooseChrom = false;
bool isBedpe = false;
+ size_t maxTries = 1000;
+ bool noOverlapping = false;
+ bool allowBeyondChromEnd = false;
for(int i = 1; i < argc; i++) {
@@ -111,9 +114,21 @@ int shuffle_main(int argc, char* argv[]) {
i++;
}
}
+ else if(PARAMETER_CHECK("-maxTries", 9, parameterLength)) {
+ if ((i+1) < argc) {
+ maxTries = atoi(argv[i + 1]);
+ i++;
+ }
+ }
else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
isBedpe = true;
}
+ else if(PARAMETER_CHECK("-noOverlapping", 14, parameterLength)) {
+ noOverlapping = true;
+ }
+ else if(PARAMETER_CHECK("-allowBeyondChromEnd", 20, parameterLength)) {
+ allowBeyondChromEnd = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -125,17 +140,15 @@ int shuffle_main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
showHelp = true;
}
-
- if (haveInclude && haveExclude) {
- cerr << endl << "*****" << endl << "*****ERROR: Cannot use -incl and -excl together." << endl << "*****" << endl;
- showHelp = true;
- }
if (!showHelp) {
BedShuffle *bc = new BedShuffle(bedFile, genomeFile, excludeFile,
includeFile, haveSeed, haveExclude,
- haveInclude, sameChrom, overlapFraction,
- seed, chooseChrom, isBedpe);
+ haveInclude, sameChrom,
+ overlapFraction, seed,
+ chooseChrom, isBedpe,
+ maxTries, noOverlapping,
+ !(allowBeyondChromEnd));
delete bc;
return 0;
}
@@ -187,6 +200,18 @@ void shuffle_help(void) {
cerr << "\t-bedpe\t" << "Indicate that the A file is in BEDPE format." << endl << endl;
+ cerr << "\t-maxTries\t" << "\n\t\tMax. number of attempts to find a home for a shuffled interval" << endl;
+ cerr << "\t\tin the presence of -incl or -excl." << endl;
+ cerr << "\t\tDefault = 1000." << endl;
+ cerr << "\t-noOverlapping\t" << "\n\t\tDon't allow shuffled intervals to overlap." << endl;
+
+ cerr << "\t-allowBeyondChromEnd\t" << "\n\t\tAllow shuffled intervals to be relocated to a position" << endl;
+ cerr << "\t\tin which the entire original interval cannot fit w/o exceeding" << endl;
+ cerr << "\t\tthe end of the chromosome. In this case, the end coordinate of the" << endl;
+ cerr << "\t\tshuffled interval will be set to the chromosome's length." << endl;
+ cerr << "\t\tBy default, an interval's original length must be fully-contained" << endl;
+ cerr << "\t\twithin the chromosome." << endl;
+
cerr << "Notes: " << endl;
cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
cerr << "\t <chromName><TAB><chromSize>" << endl << endl;
diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile
index ebdaba3..d63d924 100644
--- a/src/slopBed/Makefile
+++ b/src/slopBed/Makefile
@@ -6,7 +6,7 @@ BIN_DIR = ../../bin/
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedFile/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index 7de0afd..1fd1aba 100644
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -11,7 +11,7 @@
******************************************************************************/
#include "bedFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include <vector>
#include <iostream>
diff --git a/src/subtractBed/subtractBed.cpp b/src/subtractBed/subtractBed.cpp
index 0f5b429..d46ce8c 100644
--- a/src/subtractBed/subtractBed.cpp
+++ b/src/subtractBed/subtractBed.cpp
@@ -11,20 +11,21 @@
******************************************************************************/
#include "lineFileUtilities.h"
#include "subtractBed.h"
-
+#include <numeric>
/*
Constructor
*/
BedSubtract::BedSubtract(string &bedAFile, string &bedBFile,
float overlapFraction, bool sameStrand,
- bool diffStrand, bool removeAll)
+ bool diffStrand, bool removeAll, bool removeAny)
: _bedAFile(bedAFile)
, _bedBFile(bedBFile)
, _overlapFraction(overlapFraction)
, _sameStrand(sameStrand)
, _diffStrand(diffStrand)
, _removeAll(removeAll)
+ , _removeAny(removeAny)
{
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
@@ -54,7 +55,6 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
vector<BED>::const_iterator h = hits.begin();
vector<BED>::const_iterator hitsEnd = hits.end();
for (; h != hitsEnd; ++h) {
-
int s = max(a.start, h->start);
int e = min(a.end, h->end);
int overlapBases = (e - s);
@@ -69,7 +69,7 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
numOverlaps++;
numConsumedByB++;
}
- else if ( overlap >= _overlapFraction ) {
+ else if ( overlap >= _overlapFraction || _removeAny) {
numOverlaps++;
bOverlaps.push_back(*h);
}
@@ -80,7 +80,7 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
// no overlap found, so just report A as-is.
_bedA->reportBedNewLine(a);
}
- else if (numOverlaps == 1) {
+ else if ((numOverlaps == 1) && (!_removeAny)) {
// one overlap found. only need to look at the single
// entry in bOverlaps.
@@ -116,14 +116,17 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
}
}
}
- else if (numOverlaps > 1) {
+ else if ((numOverlaps > 1) || _removeAny) {
// multiple overlapz found. look at all the hits
// and figure out which bases in A survived. then
// report the contigous intervals that survived.
vector<bool> aKeep(a.end - a.start, true);
- if ((numConsumedByB == 0) && (_removeAll == false)) {
+ if ((numConsumedByB == 0)) {
+ if(_removeAll){ return; }
+
+ // if there's any overlap, then we don't report.
// track the number of hit starts and ends at each position in A
for (vector<BED>::iterator h = bOverlaps.begin();
h != bOverlaps.end();
@@ -136,6 +139,14 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
aKeep[i-a.start-1] = false;
}
}
+ if (_removeAny){
+ int asum = std::accumulate(aKeep.rbegin(), aKeep.rend(), 0);
+ float afrac = 1.0 - (float)asum / aKeep.size();
+ if(afrac > _overlapFraction){ return ; }
+ for (unsigned int i = 0; i < aKeep.size(); ++i) {
+ aKeep[i] = true;
+ }
+ }
// report the remaining blocks.
for (unsigned int i = 0; i < aKeep.size(); ++i) {
if (aKeep[i] == true) {
diff --git a/src/subtractBed/subtractBed.h b/src/subtractBed/subtractBed.h
index cb49a17..05dd2a7 100644
--- a/src/subtractBed/subtractBed.h
+++ b/src/subtractBed/subtractBed.h
@@ -29,7 +29,7 @@ public:
// constructor
BedSubtract(string &bedAFile, string &bedBFile,
float overlapFraction, bool sameStrand,
- bool diffStrand, bool removeAll);
+ bool diffStrand, bool removeAll, bool removeAny);
// destructor
~BedSubtract(void);
@@ -44,6 +44,7 @@ private:
bool _sameStrand;
bool _diffStrand;
bool _removeAll;
+ bool _removeAny;
// instances of bed file class.
BedFile *_bedA, *_bedB;
diff --git a/src/subtractBed/subtractMain.cpp b/src/subtractBed/subtractMain.cpp
index f543a94..ba7ff64 100644
--- a/src/subtractBed/subtractMain.cpp
+++ b/src/subtractBed/subtractMain.cpp
@@ -44,6 +44,7 @@ int subtract_main(int argc, char* argv[]) {
bool sameStrand = false;
bool diffStrand = false;
bool removeAll = false;
+ bool removeAny = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -94,6 +95,9 @@ int subtract_main(int argc, char* argv[]) {
else if (PARAMETER_CHECK("-A", 2, parameterLength)) {
removeAll = true;
}
+ else if (PARAMETER_CHECK("-N", 2, parameterLength)) {
+ removeAny = true;
+ }
else {
cerr << endl
<< "*****ERROR: Unrecognized parameter: "
@@ -109,10 +113,14 @@ int subtract_main(int argc, char* argv[]) {
<< endl << "*****" << endl;
showHelp = true;
}
-
+ if (removeAny && !haveFraction){
+ cerr << endl << "*****" << endl
+ << "*****WARNING: -N is no different from -A without -f"
+ << endl << "*****" << endl;
+ }
if (sameStrand && diffStrand) {
cerr << endl << "*****" << endl
- << "*****ERROR: Request either -s OR -S, not both."
+ << "*****ERROR: Request either -s OR -S, not both."
<< endl << "*****" << endl;
showHelp = true;
}
@@ -121,7 +129,7 @@ int subtract_main(int argc, char* argv[]) {
BedSubtract *bs = new BedSubtract(bedAFile, bedBFile,
overlapFraction, sameStrand,
- diffStrand, removeAll);
+ diffStrand, removeAll, removeAny);
delete bs;
return 0;
}
@@ -156,6 +164,9 @@ void subtract_help(void) {
cerr << "\t-A\t" << "Remove entire feature if any overlap. That is, by default," << endl;
cerr << "\t\tonly subtract the portion of A that overlaps B. Here, if" << endl;
cerr << "\t\tany overlap is found (or -f amount), the entire feature is removed." << endl << endl;
+
+ cerr << "\t-N\t" << "Same as -A except when used with -f, the amount is the sum" << endl;
+ cerr << "\t\tof all features (not any single feature)." << endl << endl;
// end the program here
exit(1);
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index 5c7590f..7258c60 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -33,7 +33,6 @@ TagBam::TagBam(const string &bamFile, const vector<string> &annoFileNames,
// destroy and delete the open file pointers
TagBam::~TagBam(void) {
- delete _bed;
CloseAnnoFiles();
}
@@ -123,7 +122,7 @@ void TagBam::Tag() {
else if (_useNames && !_useScores && !_useIntervals) {
anno->allHits(a.chrom, a.start, a.end, a.strand,
hits, _sameStrand, _diffStrand, 0.0, false);
- for (size_t j = 0; j < hits.size(); ++i) {
+ for (size_t j = 0; j < hits.size(); ++j) {
annotations << hits[j].name;
if (j < hits.size() - 1) annotations << ",";
}
diff --git a/src/tagBam/tagBam.h b/src/tagBam/tagBam.h
index 6a5e0cb..22d8567 100644
--- a/src/tagBam/tagBam.h
+++ b/src/tagBam/tagBam.h
@@ -59,7 +59,6 @@ private:
string _tag;
// instance of a bed file class.
- BedFile *_bed;
vector<BedFile*> _annoFiles;
// should we use the name field from the annotation files?
diff --git a/src/unionBedGraphs/Makefile b/src/unionBedGraphs/Makefile
index 1d255d0..b0c0d8d 100755
--- a/src/unionBedGraphs/Makefile
+++ b/src/unionBedGraphs/Makefile
@@ -7,7 +7,7 @@ BIN_DIR = ../../bin/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/bedGraphFile/ \
-I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/genomeFile/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/Point/ \
diff --git a/src/unionBedGraphs/unionBedGraphs.h b/src/unionBedGraphs/unionBedGraphs.h
index 25cbe4e..c0f5929 100644
--- a/src/unionBedGraphs/unionBedGraphs.h
+++ b/src/unionBedGraphs/unionBedGraphs.h
@@ -16,7 +16,7 @@
#include <vector>
#include <string>
#include "bedGraphFile.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "Point.h"
class UnionBedGraphs
diff --git a/src/unionBedGraphs/unionBedGraphsMain.cpp b/src/unionBedGraphs/unionBedGraphsMain.cpp
index 6411adf..46d3618 100644
--- a/src/unionBedGraphs/unionBedGraphsMain.cpp
+++ b/src/unionBedGraphs/unionBedGraphsMain.cpp
@@ -19,7 +19,7 @@
#include <getopt.h>
#include <libgen.h> //for basename()
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "unionBedGraphs.h"
#include "version.h"
diff --git a/src/utils/BamTools/.gitignore b/src/utils/BamTools/.gitignore
new file mode 100644
index 0000000..349cf4e
--- /dev/null
+++ b/src/utils/BamTools/.gitignore
@@ -0,0 +1,2 @@
+include
+lib
diff --git a/src/utils/BamTools/src/api/BamAlignment.h b/src/utils/BamTools/src/api/BamAlignment.h
index a2349ea..fb1e872 100644
--- a/src/utils/BamTools/src/api/BamAlignment.h
+++ b/src/utils/BamTools/src/api/BamAlignment.h
@@ -139,7 +139,9 @@ struct API_EXPORT BamAlignment {
unsigned int& numBytesParsed) const;
// internal data
- private:
+ public: //had to change this from private.
+ //needed to expose some members of support data that
+ //were otherwise inaccessible when using only core alignments.
struct BamAlignmentSupportData {
@@ -163,6 +165,7 @@ struct API_EXPORT BamAlignment {
BamAlignmentSupportData SupportData;
friend class Internal::BamReaderPrivate;
friend class Internal::BamWriterPrivate;
+ friend class BamFileReader;
mutable std::string ErrorString; // mutable to allow updates even in logically const methods
//! \endinternal
diff --git a/src/utils/BamTools/src/api/BamReader.cpp b/src/utils/BamTools/src/api/BamReader.cpp
index ae2adec..b92c713 100644
--- a/src/utils/BamTools/src/api/BamReader.cpp
+++ b/src/utils/BamTools/src/api/BamReader.cpp
@@ -259,6 +259,11 @@ bool BamReader::Open(const std::string& filename) {
return d->Open(filename);
}
+bool BamReader::OpenStream(std::istream* stream) {
+ return d->OpenStream(stream);
+}
+
+
/*! \fn bool BamReader::OpenIndex(const std::string& indexFilename)
\brief Opens a BAM index file.
diff --git a/src/utils/BamTools/src/api/BamReader.h b/src/utils/BamTools/src/api/BamReader.h
index fb9064d..5660040 100644
--- a/src/utils/BamTools/src/api/BamReader.h
+++ b/src/utils/BamTools/src/api/BamReader.h
@@ -46,6 +46,8 @@ class API_EXPORT BamReader {
bool Jump(int refID, int position = 0);
// opens a BAM file
bool Open(const std::string& filename);
+ bool OpenStream(std::istream* stream);
+
// returns internal file pointer to beginning of alignment data
bool Rewind(void);
// sets the target region of interest
diff --git a/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp b/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
index 75d7279..70782a7 100644
--- a/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
+++ b/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
@@ -388,6 +388,35 @@ bool BamReaderPrivate::Open(const string& filename) {
}
}
+bool BamReaderPrivate::OpenStream(std::istream* stream) {
+
+ try {
+
+ // make sure we're starting with fresh state
+ Close();
+
+ // open BgzfStream
+ m_stream.OpenStream(stream, IBamIODevice::ReadOnly);
+
+ // load BAM metadata
+ LoadHeaderData();
+ LoadReferenceData();
+
+ // store "filename" & offset of first alignment
+ m_filename = "stream"; // or whatever
+ m_alignmentsBeginOffset = m_stream.Tell();
+
+ // return success
+ return true;
+
+ } catch ( BamException& e ) {
+ const string error = e.what();
+ const string message = string("could not open input stream: \n\t") + error;
+ SetErrorString("BamReader::Open", message);
+ return false;
+ }
+}
+
bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
if ( m_randomAccessController.OpenIndex(indexFilename, this) )
diff --git a/src/utils/BamTools/src/api/internal/bam/BamReader_p.h b/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
index e8db646..3164d6f 100644
--- a/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
+++ b/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
@@ -47,6 +47,7 @@ class BamReaderPrivate {
const std::string Filename(void) const;
bool IsOpen(void) const;
bool Open(const std::string& filename);
+ bool OpenStream(std::istream* stream);
bool Rewind(void);
bool SetRegion(const BamRegion& region);
diff --git a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
index f9c7694..a1fdd3d 100644
--- a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
@@ -12,6 +12,8 @@
#include "api/internal/io/BamFtp_p.h"
#include "api/internal/io/BamHttp_p.h"
#include "api/internal/io/BamPipe_p.h"
+#include "api/internal/io/StdStreamDevice_p.h"
+
using namespace BamTools;
using namespace BamTools::Internal;
@@ -35,3 +37,9 @@ IBamIODevice* BamDeviceFactory::CreateDevice(const string& source) {
// otherwise assume a "normal" file
return new BamFile(source);
}
+
+IBamIODevice* BamDeviceFactory::CreateDevice(std::istream *stream) {
+ // compile-time sanity check
+ BT_ASSERT_X( stream, "BamDeviceFactory::CreateDevice - null input stream");
+ return new StdStreamDevice(stream);
+}
diff --git a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
index 1d48533..00bb07d 100644
--- a/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
+++ b/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
@@ -29,6 +29,7 @@ namespace Internal {
class BamDeviceFactory {
public:
static IBamIODevice* CreateDevice(const std::string& source);
+ static IBamIODevice* CreateDevice(std::istream *stream);
};
} // namespace Internal
diff --git a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
index 7f73d67..fe90e5f 100644
--- a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
+++ b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
@@ -286,6 +286,28 @@ void BgzfStream::Open(const string& filename, const IBamIODevice::OpenMode mode)
}
}
+void BgzfStream::OpenStream(std::istream* stream, const IBamIODevice::OpenMode mode) {
+
+ // close current device if necessary
+ Close();
+ BT_ASSERT_X( (m_device == 0), "BgzfStream::Open() - unable to properly close previous IO device" );
+
+ // run-time sanity check
+ if ( stream == NULL )
+ throw BamException("BgzfStream::Open", "null input stream");
+
+ // retrieve new IO device for std::stream*
+ m_device = BamDeviceFactory::CreateDevice(stream);
+ BT_ASSERT_X( m_device, "BgzfStream::Open() - unable to create IO device from stream" );
+
+ // if device fails to open
+ if ( !m_device->Open(mode) ) {
+ const string deviceError = m_device->GetErrorString();
+ const string message = string("could not open BGZF stream: \n\t") + deviceError;
+ throw BamException("BgzfStream::Open", message);
+ }
+}
+
// reads BGZF data into a byte buffer
size_t BgzfStream::Read(char* data, const size_t dataLength) {
@@ -345,6 +367,8 @@ void BgzfStream::ReadBlock(void) {
// read block header from file
char header[Constants::BGZF_BLOCK_HEADER_LENGTH];
+ memset(header, 0, Constants::BGZF_BLOCK_HEADER_LENGTH);
+
int64_t numBytesRead = m_device->Read(header, Constants::BGZF_BLOCK_HEADER_LENGTH);
// check for device error
diff --git a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
index 47b3609..9297820 100644
--- a/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
+++ b/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
@@ -45,6 +45,8 @@ class BgzfStream {
bool IsOpen(void) const;
// opens the BGZF file
void Open(const std::string& filename, const IBamIODevice::OpenMode mode);
+
+ void OpenStream(std::istream* stream, const IBamIODevice::OpenMode mode);
// reads BGZF data into a byte buffer
size_t Read(char* data, const size_t dataLength);
// seek to position in BGZF file
diff --git a/src/utils/BamTools/src/api/internal/io/NetUnix_p.h b/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
index f06c4df..8cf75f8 100644
--- a/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
+++ b/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
@@ -23,7 +23,6 @@
#ifndef _WIN32 // <-- source files only include the proper Net*_p.h, but this is a double-check
#include <arpa/inet.h>
-#include <netinet/in.h>
#include <sys/ioctl.h>
#include <sys/socket.h>
#include <sys/stat.h>
diff --git a/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h b/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h
new file mode 100644
index 0000000..a957c26
--- /dev/null
+++ b/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h
@@ -0,0 +1,54 @@
+/*
+ * StdStreamDevice_p.h
+ *
+ * Created on: Apr 24, 2013
+ * Author: nek3d
+ */
+
+#ifndef STDSTREAMDEVICE_P_H_
+#define STDSTREAMDEVICE_P_H_
+
+//NOTE: The stream management methods in this class are placeholders. The class is not intended to manage a
+// a stream. Rather, it is intended to accept a stream that is managed elsewhere, and allow that stream to
+//be used with bamtools.
+
+#include "api/IBamIODevice.h"
+#include <cstring> //for strlen
+#include <istream>
+
+namespace BamTools {
+namespace Internal {
+
+class StdStreamDevice : public IBamIODevice {
+
+ // ctor & dtor
+ public:
+ StdStreamDevice(std::istream *stream) : m_stream(stream) {
+ IBamIODevice::m_mode = IBamIODevice::ReadOnly;
+ }
+ ~StdStreamDevice() {}
+
+ // IBamIODevice implementation
+ public:
+ void Close(void) {}
+ bool IsOpen(void) const { return true; } // assume stream passed in is always open.
+ bool IsRandomAccess(void) const { return false; }
+ bool Open(const IBamIODevice::OpenMode mode) { return true; } //stream is assumed opened by caller.
+ int64_t Read(char* data, const unsigned int numBytes) {
+ m_stream->read(data, numBytes);
+ return (int64_t)(numBytes);
+ }
+ bool Seek(const int64_t& position, const int origin = SEEK_SET) { return false; }
+
+ //Not sure what Tell and Write should do for streams.
+ int64_t Tell(void) const { return 0; }
+ int64_t Write(const char* data, const unsigned int numBytes) { return 0; }
+
+ private:
+ std::istream* m_stream;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif /* STDSTREAMDEVICE_P_H_ */
diff --git a/src/utils/BinTree/BinTree.cpp b/src/utils/BinTree/BinTree.cpp
new file mode 100644
index 0000000..54696f6
--- /dev/null
+++ b/src/utils/BinTree/BinTree.cpp
@@ -0,0 +1,220 @@
+#include "BinTree.h"
+#include "FileRecordMgr.h"
+
+
+BinTree::BinTree(ContextIntersect *context)
+: _databaseFile(NULL),
+ _context(context),
+ _binOffsetsExtended(NULL),
+ _showBinMetrics(false),
+ _maxBinNumFound(0)
+ {
+ _binOffsetsExtended = new uint32_t[NUM_BIN_LEVELS];
+ memset(_binOffsetsExtended, 0, NUM_BIN_LEVELS * sizeof(uint32_t));
+
+ //start at idx 1, because the memset above already initialized
+ //the first idx to zero, which is what we want.
+ for (uint32_t i= 1; i < NUM_BIN_LEVELS; i++) {
+ _binOffsetsExtended[i] = _binOffsetsExtended[i-1] + (1 << ((NUM_BIN_LEVELS - i -1) * 3));
+ }
+}
+
+BinTree::~BinTree() {
+ //TBD: pass all elements in tree back to FRM for proper cleanup/deletion
+ for (mainMapType::iterator mainIter = _mainMap.begin(); mainIter != _mainMap.end(); mainIter++) {
+ allBinsType bins = mainIter->second;
+ if (bins == NULL) {
+ fprintf(stderr, "ERROR: In BinTree destructor: found chromosome with NULL bin array.\n");
+ continue;
+ }
+ if (!_showBinMetrics) { //don't clean up bins when simply reporting metrics.
+
+ for (uint32_t i=0; i < NUM_BINS; i++) {
+ binType bin = bins[i];
+ if (bin == NULL) {
+ continue;
+ }
+ for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
+ const Record *record = listIter->value();
+ _databaseFile->deleteRecord(record);
+ }
+ delete bin;
+ bin = NULL;
+ }
+ }
+ delete [] bins;
+ bins = NULL;
+ }
+ delete [] _binOffsetsExtended;
+
+ if (_showBinMetrics) {
+ map<int, int> hitsHistogram;
+ FILE *fp = fopen("BinsHitFile.txt", "w");
+ fprintf(fp, "The largest bin was %u\n", _maxBinNumFound);
+ fprintf(fp, "There were %d different bins hit by database.\n", (int)_binsHit.size());
+ for (map<uint32_t, int>::iterator binIter = _binsHit.begin(); binIter != _binsHit.end(); binIter++) {
+ uint32_t binNum = binIter->first;
+ int numHits = binIter->second;
+ fprintf(fp, "%u\t%d\n", binNum, numHits);
+ hitsHistogram[numHits]++;
+ }
+ fclose(fp);
+ fp = fopen("BinHitsHistogram.txt", "w");
+ fprintf(fp, "NumHits\tNumBins\n");
+ for (map<int, int>::iterator histIter = hitsHistogram.begin(); histIter != hitsHistogram.end(); histIter++) {
+ fprintf(fp, "%d\t%d\n", histIter->first, histIter->second);
+ }
+ fclose(fp);
+ }
+}
+
+void BinTree::loadDB()
+{
+ _databaseFile = _context->getFile(_context->getDatabaseFileIdx());
+
+ Record *record = NULL;
+ while (!_databaseFile->eof()) {
+ record = _databaseFile->allocateAndGetNextRecord();
+ //In addition to NULL records, we also don't want to add unmapped reads.
+ if (record == NULL || record->isUnmapped()) {
+ continue;
+ }
+
+ if (!addRecordToTree(record)) {
+ fprintf(stderr, "ERROR: Unable to add record to tree.\n");
+ _databaseFile->close();
+ exit(1);
+ }
+ }
+ _databaseFile->close();
+
+ //TBD: give ERROR and return false if tree is empty.
+ if (_mainMap.empty()) {
+ fprintf(stderr, "ERROR: Tree is empty, no records added.\n");
+ exit(1);
+ }
+}
+
+void BinTree::getHits(Record *record, RecordKeyList &hitSet)
+{
+ if (_showBinMetrics) {
+ return; //don't care about query entries just yet.
+ }
+ if (record->isUnmapped()) {
+ return;
+ }
+ const QuickString &chr = record->getChrName();
+ mainMapType::iterator mainIter = _mainMap.find(chr);
+ if (mainIter == _mainMap.end()) {
+ //given chrom not even in map.
+ return;
+ }
+
+ uint32_t startBin = 0;
+ uint32_t endBin = 0;
+
+ uint32_t startPos = record->getStartPos();
+ uint32_t endPos = record->getEndPos();
+
+ startBin = (startPos >> _binFirstShift);
+ endBin = ((endPos-1) >> _binFirstShift);
+
+
+ const allBinsType bins = mainIter->second;
+
+ /* SYNOPSIS:
+ 1. We loop through each UCSC BIN level for feature A's chrom.
+ 2. For each BIN, we loop through each B feature and add it to
+ hits if it meets all of the user's requests, which include:
+ (a) overlap fractio, (b) strandedness, (c) reciprocal overlap
+ */
+ for (uint32_t i = 0; i < NUM_BIN_LEVELS; i++) {
+ uint32_t offset = _binOffsetsExtended[i];
+ for (uint32_t j = (startBin+offset); j <= (endBin+offset); j++) {
+
+ // move to the next bin if this one is empty
+ const binType &bin = bins[j];
+ if (bin == NULL) {
+ //no list of records in this bin.
+ continue;
+ }
+ if (bin->empty()) {
+ //bin has list, but it's empty.
+ //Actually, this should never happen, so throw an error.
+ fprintf(stderr, "ERROR: found empty list for bin %u of chromosome %s\n",
+ j, chr.c_str());
+ continue;
+ }
+ for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
+ const Record *dbRec = listIter->value();
+ if (record->intersects(dbRec, _context->getSameStrand(), _context->getDiffStrand(),
+ _context->getOverlapFraction(), _context->getReciprocal())) {
+ hitSet.push_back(dbRec);
+ }
+ }
+ }
+ startBin >>= _binNextShift;
+ endBin >>= _binNextShift;
+ }
+}
+
+bool BinTree::addRecordToTree(const Record *record)
+{
+ // Get chr, bin. allocate all bins and single bins as needed.
+ const QuickString &chr = record->getChrName();
+ uint32_t startPos = (uint32_t)(record->getStartPos());
+ uint32_t endPos = (uint32_t)(record->getEndPos());
+
+ //is this chr currently in the main map?
+ allBinsType bins = NULL;
+ mainMapType::iterator mainIter = _mainMap.find(chr);
+ if (mainIter == _mainMap.end()) {
+ //this is a new chr NOT currently in the map.
+ bins = new binType[NUM_BINS];
+ memset(bins, 0, NUM_BINS * sizeof(binType));
+ _mainMap[chr] = bins;
+ } else {
+ bins = mainIter->second;
+ }
+ uint32_t binNum = getBin(startPos, endPos);
+
+ if (_showBinMetrics) {
+ if (binNum > _maxBinNumFound) {
+ _maxBinNumFound = binNum;
+ }
+ _binsHit[binNum]++;
+ return true;
+ }
+
+ if (binNum < 0 || binNum >= NUM_BINS) {
+ fprintf(stderr, "ERROR: Received illegal bin number %u from getBin call.\n", binNum);
+ return false;
+ }
+ binType &bin = bins[binNum];
+ if (bin == NULL) {
+ bin = new innerListType;
+ }
+ bin->push_back(record);
+
+ return true;
+}
+
+uint32_t BinTree::getBin(const Record *record) const {
+ return getBin((uint32_t)(record->getStartPos()), (uint32_t)(record->getEndPos()));
+}
+
+uint32_t BinTree::getBin(uint32_t start, uint32_t end) const {
+ --end;
+ start >>= _binFirstShift;
+ end >>= _binFirstShift;
+
+ for (uint32_t i = 0; i < NUM_BIN_LEVELS; ++i) {
+ if (start == end) {
+ return _binOffsetsExtended[i] + start;
+ }
+ start >>= _binNextShift;
+ end >>= _binNextShift;
+ }
+ //failure
+ return -1;
+}
diff --git a/src/utils/BinTree/BinTree.h b/src/utils/BinTree/BinTree.h
new file mode 100644
index 0000000..ce15c48
--- /dev/null
+++ b/src/utils/BinTree/BinTree.h
@@ -0,0 +1,75 @@
+/*
+ * BinTree.h
+ *
+ * Created on: Jan 5, 2013
+ * Author: nek3d
+ */
+
+#ifndef BINTREE_H_
+#define BINTREE_H_
+
+using namespace std;
+
+#include <stdint.h>
+#include <string>
+#include <set>
+#include <map>
+
+#include "QuickString.h"
+#include "RecordKeyList.h"
+#include "ContextIntersect.h"
+
+class FileRecordMgr;
+class Record;
+
+class BinTree {
+public:
+ BinTree(ContextIntersect *context);
+
+ ~BinTree();
+ void loadDB();
+ void getHits(Record *record, RecordKeyList &hitSet);
+
+private:
+
+ FileRecordMgr *_databaseFile;
+ ContextIntersect *_context;
+
+ //
+ // BIN HANDLING
+ //
+ static const uint32_t NUM_BINS = 37450;
+ static const uint32_t NUM_BIN_LEVELS = 7;
+
+ // bins range in size from 16kb to 512Mb
+ // Bin 0 spans 512Mbp, # Level 1
+ // Bins 1-8 span 64Mbp, # Level 2
+ // Bins 9-72 span 8Mbp, # Level 3
+ // Bins 73-584 span 1Mbp # Level 4
+ // Bins 585-4680 span 128Kbp # Level 5
+ // Bins 4681-37449 span 16Kbp # Level 6
+ uint32_t *_binOffsetsExtended;
+ static const uint32_t _binFirstShift = 14; /* How much to shift to get to finest bin. */
+ static const uint32_t _binNextShift = 3; /* How much to shift to get to next larger bin. */
+
+ typedef BTlist<const Record *> innerListType;
+ typedef const BTlistNode<const Record *> * innerListIterType;
+ typedef innerListType * binType;
+ typedef binType * allBinsType;
+ typedef QuickString mainKeyType;
+ typedef map<mainKeyType, allBinsType> mainMapType;
+ mainMapType _mainMap;
+
+ bool _showBinMetrics;
+ uint32_t _maxBinNumFound;
+ map<uint32_t, int> _binsHit;
+
+ bool addRecordToTree(const Record *);
+ uint32_t getBin(uint32_t start, uint32_t end) const;
+ uint32_t getBin(const Record *record) const;
+
+
+};
+
+
+#endif /* BINTREE_H_ */
diff --git a/src/utils/fileType/Makefile b/src/utils/BinTree/Makefile
similarity index 50%
copy from src/utils/fileType/Makefile
copy to src/utils/BinTree/Makefile
index 91585d5..de04c81 100644
--- a/src/utils/fileType/Makefile
+++ b/src/utils/BinTree/Makefile
@@ -4,14 +4,23 @@ UTILITIES_DIR = ../../utils/
# -------------------
# define our includes
# -------------------
-INCLUDES =
-
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= fileType.cpp fileType.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=
+SOURCES= BinTree.cpp BinTree.h
+OBJECTS= BinTree.o
+_EXT_OBJECTS=
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -24,6 +33,6 @@ $(EXT_OBJECTS):
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+ @rm -f $(OBJ_DIR)/BinTree.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/BlockedIntervals/Makefile b/src/utils/BlockedIntervals/Makefile
index 0286a6f..ec82878 100644
--- a/src/utils/BlockedIntervals/Makefile
+++ b/src/utils/BlockedIntervals/Makefile
@@ -12,7 +12,7 @@ INCLUDES = -I$(UTILITIES_DIR)/BamTools/include \
# define our source and object files
# ----------------------------------
SOURCES= BlockedIntervals.cpp BlockedIntervals.h
-OBJECTS= $(SOURCES:.cpp=.o)
+OBJECTS= BlockedIntervals.o
_EXT_OBJECTS=bedFile.o fileType.o gzstream.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -32,4 +32,4 @@ clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
new file mode 100644
index 0000000..cd30b20
--- /dev/null
+++ b/src/utils/Contexts/ContextBase.cpp
@@ -0,0 +1,365 @@
+/*
+ * ContextBase.cpp
+ *
+ * Created on: Feb 12, 2013
+ * Author: nek3d
+ */
+
+#include "ContextBase.h"
+#include <unistd.h>
+#include <sys/types.h>
+
+ContextBase::ContextBase()
+:
+ _program(UNSPECIFIED_PROGRAM),
+ _allFilesOpened(false),
+ _useMergedIntervals(false),
+ _genomeFile(NULL),
+ _outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
+ _outputTypeDetermined(false),
+ _skipFirstArgs(0),
+ _showHelp(false),
+ _obeySplits(false),
+ _uncompressedBam(false),
+ _useBufferedOutput(true),
+ _anyHit(false),
+ _noHit(false),
+ _writeA(false),
+ _writeB(false),
+ _leftJoin(false),
+ _writeCount(false),
+ _writeOverlap(false),
+ _writeAllOverlap(false),
+ _haveFraction(false),
+ _overlapFraction(1E-9),
+ _reciprocal(false),
+ _sameStrand(false),
+ _diffStrand(false),
+ _sortedInput(false),
+ _printHeader(false),
+ _printable(true),
+ _explicitBedOutput(false),
+ _queryFileIdx(-1),
+ _databaseFileIdx(-1),
+ _bamHeaderAndRefIdx(-1),
+ _maxNumDatabaseFields(0),
+ _useFullBamTags(false),
+ _reportCount(false),
+ _maxDistance(0),
+ _reportNames(false),
+ _reportScores(false),
+ _numOutputRecords(0),
+ _hasConstantSeed(false),
+ _seed(0),
+ _forwardOnly(false),
+ _reverseOnly(false)
+{
+ _programNames["intersect"] = INTERSECT;
+ _programNames["sample"] = SAMPLE;
+ _programNames["map"] = MAP;
+
+ _validScoreOps.insert("sum");
+ _validScoreOps.insert("max");
+ _validScoreOps.insert("min");
+ _validScoreOps.insert("mean");
+ _validScoreOps.insert("mode");
+ _validScoreOps.insert("median");
+ _validScoreOps.insert("antimode");
+ _validScoreOps.insert("collapse");
+}
+
+ContextBase::~ContextBase()
+{
+ delete _genomeFile;
+ _genomeFile = NULL;
+
+ //close all files and delete FRM objects.
+ for (int i=0; i < (int)_files.size(); i++) {
+ _files[i]->close();
+ delete _files[i];
+ _files[i] = NULL;
+ }
+}
+
+bool ContextBase::determineOutputType() {
+ if (_outputTypeDetermined) {
+ return true;
+ }
+ //test whether output should be BED or BAM.
+ //If the user explicitly requested BED, then it's BED.
+ if (getExplicitBedOutput()) {
+ setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
+ _outputTypeDetermined = true;
+ return true;
+ }
+
+ //Otherwise, if there are any BAM files in the input,
+ //then the output should be BAM.
+ for (_i = 0; _i < (int)_files.size(); _i++) {
+ if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
+ _bamHeaderAndRefIdx = _i;
+ _outputTypeDetermined = true;
+ return true;
+ }
+ }
+
+ //Okay, it's bed.
+ setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
+ _outputTypeDetermined = true;
+ return true;
+
+
+}
+
+void ContextBase::openGenomeFile(const QuickString &genomeFilename)
+{
+ _genomeFile = new NewGenomeFile(genomeFilename.c_str());
+}
+
+void ContextBase::openGenomeFile(const BamTools::RefVector &refVector)
+{
+ _genomeFile = new NewGenomeFile(refVector);
+}
+
+bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ if (isUsed(_i - _skipFirstArgs)) {
+ continue;
+ }
+
+ if (strcmp(_argv[_i], "-i") == 0) {
+ if (!handle_i()) return false;
+ }
+ else if (strcmp(_argv[_i], "-g") == 0) {
+ if (!handle_g()) return false;
+ }
+ else if ((strcmp(_argv[_i], "-h") == 0) || (strcmp(_argv[_i], "--help") == 0)) {
+ if (!handle_h()) return false;
+ }
+ else if (strcmp(_argv[_i], "-split") == 0) {
+ if (!handle_split()) return false;
+ }
+ else if (strcmp(_argv[_i], "-bed") == 0) {
+ if (!handle_bed()) return false;
+ }
+ else if (strcmp(_argv[_i], "-ubam") == 0) {
+ if (!handle_ubam()) return false;
+ }
+ else if (strcmp(_argv[_i], "-fbam") == 0) {
+ if (!handle_fbam()) return false;
+ }
+ else if(strcmp(_argv[_i], "-sorted") == 0) {
+ if (!handle_sorted()) return false;
+ }
+ else if (strcmp(_argv[_i], "-nobuf") == 0) {
+ if (!handle_nobuf()) return false;
+ }
+ else if (strcmp(_argv[_i], "-header") == 0) {
+ if (!handle_header()) return false;
+ }
+ else if (strcmp(_argv[_i], "-n") == 0) {
+ if (!handle_n()) return false;
+ }
+ else if (strcmp(_argv[_i], "-seed") == 0) {
+ if (!handle_seed()) return false;
+ }
+ }
+ return true;
+}
+
+bool ContextBase::isValidState()
+{
+ if (!openFiles()) {
+ return false;
+ }
+ if (!cmdArgsValid()) {
+ return false;
+ }
+ if (!determineOutputType()) {
+ return false;
+ }
+ return true;
+}
+
+
+bool ContextBase::cmdArgsValid()
+{
+ bool retval = true;
+ for (_i = _skipFirstArgs; _i < _argc; _i++) {
+ if (!isUsed(_i - _skipFirstArgs)) {
+ _errorMsg += "\n***** ERROR: Unrecognized parameter: ";
+ _errorMsg += _argv[_i];
+ _errorMsg += " *****";
+ retval = false;
+ }
+ }
+ return retval;
+}
+
+bool ContextBase::openFiles() {
+
+ //Make a vector of FileRecordMgr objects by going through the vector
+ //of filenames and opening each one.
+ if (_allFilesOpened) {
+ return true;
+ }
+ _files.resize(_fileNames.size());
+
+ for (int i = 0; i < (int)_fileNames.size(); i++) {
+ FileRecordMgr *frm = new FileRecordMgr(_fileNames[i], _sortedInput);
+ if (hasGenomeFile()) {
+ frm->setGenomeFile(_genomeFile);
+ }
+ frm->setFullBamFlags(_useFullBamTags);
+ if (!frm->open()) {
+ return false;
+ }
+ _files[i] = frm;
+ }
+ _allFilesOpened = true;
+ return true;
+}
+
+int ContextBase::getBamHeaderAndRefIdx() {
+ if (_bamHeaderAndRefIdx != -1) {
+ //already found which BAM file to use for the header
+ return _bamHeaderAndRefIdx;
+ }
+ if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ _bamHeaderAndRefIdx = _queryFileIdx;
+ } else {
+ _bamHeaderAndRefIdx = _databaseFileIdx;
+ }
+ return _bamHeaderAndRefIdx;
+}
+
+int ContextBase::getUnspecifiedSeed()
+{
+ // thanks to Rob Long for the tip.
+ _seed = (unsigned)time(0)+(unsigned)getpid();
+ srand(_seed);
+ return _seed;
+}
+
+bool ContextBase::handle_bed()
+{
+ setExplicitBedOutput(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_fbam()
+{
+ setUseFullBamTags(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_g()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -g option given, but no genome file specified. *****";
+ return false;
+ }
+ openGenomeFile(_argv[_i+1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_h()
+{
+ setShowHelp(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_header()
+{
+ setPrintHeader(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_i()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -i option given, but no input file specified. *****";
+ return false;
+ }
+ addInputFile(_argv[_i+1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_n()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -n option given, but no number of output records specified. *****";
+ return false;
+ }
+ setNumOutputRecords(atoi(_argv[_i + 1]));
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_nobuf()
+{
+ setUseBufferedOutput(false);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_seed()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -seed option given, but no seed specified. *****";
+ return false;
+ }
+ _hasConstantSeed = true;
+ _seed = atoi(_argv[_i+1]);
+ srand(_seed);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_split()
+{
+ setObeySplits(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_sorted()
+{
+ setSortedInput(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextBase::handle_ubam()
+{
+ setUncompressedBam(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
diff --git a/src/utils/Contexts/ContextBase.h b/src/utils/Contexts/ContextBase.h
new file mode 100644
index 0000000..872193f
--- /dev/null
+++ b/src/utils/Contexts/ContextBase.h
@@ -0,0 +1,236 @@
+/*
+ * ContextBase.h
+ *
+ * Created on: Feb 11, 2013
+ * Author: nek3d
+ */
+
+#ifndef CONTEXTBASE_H_
+#define CONTEXTBASE_H_
+
+
+// The Context class handles the settings for an operation,
+// such as merge, intersect, jaccard, etc.
+//
+// Settings include the input and output parameters, such as input
+// files, file types (if explicitly provided), genome files,
+// run options, output format, etc.
+
+#include <cstdlib>
+#include "version.h"
+#include "BedtoolsTypes.h"
+#include "FileRecordTypeChecker.h"
+#include "FileRecordMgr.h"
+#include "NewGenomeFile.h"
+#include "api/BamReader.h"
+#include "api/BamAux.h"
+
+
+class ContextBase {
+public:
+ ContextBase();
+ virtual ~ContextBase();
+
+ typedef FileRecordTypeChecker::FILE_TYPE ContextFileType;
+ typedef FileRecordTypeChecker::RECORD_TYPE ContextRecordType;
+
+ typedef enum {UNSPECIFIED_PROGRAM, INTERSECT, WINDOW, CLOSEST, COVERAGE, MAP, GENOMECOV, MERGE, CLUSTER,
+ COMPLEMENT, SUBTRACT, SLOP, FLANK, SORT, RANDOM, SAMPLE, SHUFFLE, ANNOTATE, MULTIINTER, UNIONBEDG, PAIRTOBED,
+ PAIRTOPAIR,BAMTOBED, BEDTOBAM, BEDTOFASTQ, BEDPETOBAM, BED12TOBED6, GETFASTA, MASKFASTA, NUC,
+ MULTICOV, TAG, JACCARD, OVERLAP, IGV, LINKS,MAKEWINDOWS, GROUPBY, EXPAND } PROGRAM_TYPE;
+
+ PROGRAM_TYPE getProgram() const { return _program; }
+ FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }
+ void setProgram(PROGRAM_TYPE program) { _program = program; }
+
+ void addInputFile(const QuickString &inputFile) { _fileNames.push_back(inputFile); }
+
+ int getNumInputFiles() const { return _fileNames.size(); }
+ const QuickString &getInputFileName(int fileNum) const { return _fileNames[fileNum]; }
+ ContextFileType getInputFileType(int fileNum) const { return _files[fileNum]->getFileType(); }
+ ContextRecordType getInputRecordType(int fileNum) const { return _files[fileNum]->getRecordType(); }
+
+ virtual bool determineOutputType();
+
+ const QuickString &getHeader(int fileIdx) { return _files[fileIdx]->getHeader(); }
+ const BamTools::RefVector &getBamReferences(int fileIdx) { return _files[fileIdx]->getBamReferences(); }
+ int getBamHeaderAndRefIdx(); //return idx of 1st query that is BAM. If none, first DB that is BAM.
+
+ bool getUseMergedIntervals() const { return _useMergedIntervals; }
+ void setUseMergedIntervals(bool val) { _useMergedIntervals = val; }
+
+ void openGenomeFile(const QuickString &genomeFilename);
+ void openGenomeFile(const BamTools::RefVector &refVector);
+ bool hasGenomeFile() const { return _genomeFile != NULL; }
+ NewGenomeFile *getGenomeFile() const { return _genomeFile; }
+
+ void setOutputFileType(ContextFileType fileType) { _outputFileType = fileType; }
+ ContextFileType getOutputFileType() const { return _outputFileType; }
+
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+
+ //isValidState checks that parameters to context are in an acceptable state.
+ // If not, the error msg string will be set with a reason why it failed.
+ virtual bool isValidState();
+ bool getShowHelp() const { return _showHelp; }
+ void setShowHelp(bool val) { _showHelp = val; }
+
+ const QuickString &getErrorMsg() const { return _errorMsg; }
+ void setErrorMessage(const QuickString &errorMsg) { _errorMsg = errorMsg; }
+
+ //split handling.
+ bool getObeySplits() const {return _obeySplits; }
+ void setObeySplits(bool val) { _obeySplits = val; }
+
+ //Decide whether output format is BED or BAM.
+ //Default is BAM if any input files are BAM.
+ bool getExplicitBedOutput() const { return _explicitBedOutput; }
+ void setExplicitBedOutput(bool val) { _explicitBedOutput = val; }
+
+ bool getUncompressedBam() const { return _uncompressedBam; }
+ void setUncompressedBam(bool val) { _uncompressedBam = val; }
+
+ bool getUseBufferedOutput() const { return _useBufferedOutput; }
+ void setUseBufferedOutput(bool val) { _useBufferedOutput = val; }
+
+ virtual bool getSortedInput() const {return _sortedInput; }
+ virtual void setSortedInput(bool val) { _sortedInput = val; }
+
+ virtual bool getPrintHeader() const {return _printHeader; }
+ virtual void setPrintHeader(bool val) { _printHeader = val; }
+
+ virtual bool getPrintable() const { return _printable; }
+ virtual void setPrintable(bool val) { _printable = val; }
+
+ virtual bool getUseFullBamTags() const { return _useFullBamTags; }
+ virtual void setUseFullBamTags(bool val) { _useFullBamTags = val; }
+
+ //
+ // MERGE METHODS
+ //
+ virtual bool getReportCount() const { return _reportCount; }
+ virtual void setReportCount(bool val) { _reportCount = val; }
+
+ virtual int getMaxDistance() const { return _maxDistance; }
+ virtual void setMaxDistance(int distance) { _maxDistance = distance; }
+
+ virtual bool getReportNames() const { return _reportNames; }
+ virtual void setReportNames(bool val) { _reportNames = val; }
+
+ virtual bool getReportScores() const { return _reportScores; }
+ virtual void setReportScores(bool val) { _reportScores = val; }
+
+ virtual const QuickString &getScoreOp() const { return _scoreOp; }
+ virtual void setScoreOp(const QuickString &op) { _scoreOp = op; }
+
+
+ // METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER
+ // OF OUTPUT RECORDS.
+ virtual int getNumOutputRecords() const { return _numOutputRecords; }
+ virtual void setNumOutputRecords(int val) { _numOutputRecords = val; }
+
+ //SEED OPS FOR APPS WITH RANDOMNESS
+ //When a seed has been specified on the command line, srand
+ //will have been already been called during command line parsing.
+ //For reference, srand is the C function that initializes the
+ //psuedo-random number generator. If a seed has not been
+ //specifified, the user may call the
+ virtual bool hasConstantSeed() const { return _hasConstantSeed; }
+ virtual int getConstantSeed() const { return _seed; }
+ virtual int getUnspecifiedSeed();
+
+ //method used by other classes to distinguish ContextBase from
+ //ContextIntersect and other derived classes that use intersection
+ //methods.
+ virtual bool hasIntersectMethods() const { return false; }
+
+protected:
+ PROGRAM_TYPE _program;
+
+ vector<QuickString> _fileNames;
+ vector<FileRecordMgr *> _files;
+ bool _allFilesOpened;
+ map<QuickString, PROGRAM_TYPE> _programNames;
+
+ bool _useMergedIntervals;
+ NewGenomeFile *_genomeFile;
+
+ ContextFileType _outputFileType;
+ bool _outputTypeDetermined;
+
+ map<int, QuickString> _headers;
+ map<int, BamTools::RefVector> _references;
+
+ QuickString _errorMsg;
+ vector<bool> _argsProcessed; //used for processing cmdLine args.
+ int _skipFirstArgs;
+ bool _showHelp;
+ bool _obeySplits;
+ bool _uncompressedBam;
+ bool _useBufferedOutput;
+
+ bool _anyHit;
+ bool _noHit;
+ bool _writeA;
+ bool _writeB;
+ bool _leftJoin;
+ bool _writeCount;
+ bool _writeOverlap;
+ bool _writeAllOverlap;
+ bool _haveFraction;
+ float _overlapFraction;
+ bool _reciprocal;
+ bool _sameStrand;
+ bool _diffStrand;
+ bool _sortedInput;
+ bool _printHeader;
+ bool _printable;
+ bool _explicitBedOutput;
+ int _queryFileIdx;
+ int _databaseFileIdx;
+ int _bamHeaderAndRefIdx;
+ int _maxNumDatabaseFields;
+ bool _useFullBamTags;
+ QuickString _columnOperation;
+ int _column;
+ QuickString _nullValue;
+ bool _reportCount;
+ int _maxDistance;
+ bool _reportNames;
+ bool _reportScores;
+ QuickString _scoreOp;
+ set<QuickString> _validScoreOps;
+
+ int _numOutputRecords;
+
+ bool _hasConstantSeed;
+ int _seed;
+ bool _forwardOnly;
+ bool _reverseOnly;
+
+ void markUsed(int i) { _argsProcessed[i] = true; }
+ bool isUsed(int i) const { return _argsProcessed[i]; }
+ bool cmdArgsValid();
+ bool openFiles();
+
+ //set cmd line params and counter, i, as members so code
+ //is more readable (as opposed to passing all 3 everywhere).
+ int _argc;
+ char **_argv;
+ int _i;
+
+ virtual bool handle_bed();
+ virtual bool handle_fbam();
+ virtual bool handle_g();
+ virtual bool handle_h();
+ virtual bool handle_header();
+ virtual bool handle_i();
+ virtual bool handle_n();
+ virtual bool handle_nobuf();
+ virtual bool handle_seed();
+ virtual bool handle_split();
+ virtual bool handle_sorted();
+ virtual bool handle_ubam();
+};
+
+#endif /* CONTEXTBASE_H_ */
diff --git a/src/utils/Contexts/ContextIntersect.cpp b/src/utils/Contexts/ContextIntersect.cpp
new file mode 100644
index 0000000..fecf51d
--- /dev/null
+++ b/src/utils/Contexts/ContextIntersect.cpp
@@ -0,0 +1,318 @@
+/*
+ * ContextIntersect.cpp
+ *
+ * Created on: Jan 6, 2014
+ * Author: nek3d
+ */
+
+#include "ContextIntersect.h"
+
+ContextIntersect::ContextIntersect()
+{
+
+}
+
+ContextIntersect::~ContextIntersect()
+{
+
+}
+
+
+bool ContextIntersect::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ if (isUsed(_i - _skipFirstArgs)) {
+ continue;
+ }
+ if (strcmp(_argv[_i], "-a") == 0) {
+ if (!handle_a()) return false;
+ }
+ else if (strcmp(_argv[_i], "-abam") == 0) {
+ if (!handle_abam()) return false;
+ }
+ else if (strcmp(_argv[_i], "-b") == 0) {
+ if (!handle_b()) return false;
+ }
+ else if (strcmp(_argv[_i], "-u") == 0) {
+ if (!handle_u()) return false;
+ }
+ else if (strcmp(_argv[_i], "-f") == 0) {
+ if (!handle_f()) return false;
+ }
+ else if (strcmp(_argv[_i], "-wa") == 0) {
+ if (!handle_wa()) return false;
+ }
+ else if (strcmp(_argv[_i], "-wao") == 0) {
+ if (!handle_wao()) return false;
+ }
+ else if (strcmp(_argv[_i], "-wb") == 0) {
+ if (!handle_wb()) return false;
+ }
+ else if (strcmp(_argv[_i], "-wo") == 0) {
+ if (!handle_wo()) return false;
+ }
+ else if (strcmp(_argv[_i], "-c") == 0) {
+ if (!handle_c()) return false;
+ }
+ else if(strcmp(_argv[_i], "-r") == 0) {
+ if (!handle_r()) return false;
+ }
+ else if (strcmp(_argv[_i], "-v") == 0) {
+ if (!handle_v()) return false;
+ }
+ else if (strcmp(_argv[_i], "-s") == 0) {
+ if (!handle_s()) return false;
+ }
+ else if (strcmp(_argv[_i], "-S") == 0) {
+ if (!handle_S()) return false;
+ }
+ else if (strcmp(_argv[_i], "-loj") == 0) {
+ if (!handle_loj()) return false;
+ }
+ }
+ return ContextBase::parseCmdArgs(argc, argv, _skipFirstArgs);
+}
+
+
+
+bool ContextIntersect::isValidState()
+{
+ if (!ContextBase::isValidState()) {
+ return false;
+ }
+
+ if (_queryFileIdx == -1 || _databaseFileIdx == -1) {
+ _errorMsg = "\n***** ERROR: query and database files not specified. *****";
+ return false;
+ }
+
+ if (getAnyHit() && getNoHit()) {
+ _errorMsg = "\n***** ERROR: request either -u for anyHit OR -v for noHit, not both. *****";
+ return false;
+ }
+ if (getWriteCount()) {
+ if (getAnyHit()) {
+ _errorMsg = "\n***** ERROR: request either -c for writeCount OR -u for anyHit, not both. *****";
+ return false;
+ } else if (getWriteB()) {
+ _errorMsg = "\n***** ERROR: request either -c for writeCount OR -wb for writeB, not both. *****";
+ return false;
+ } else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
+ _errorMsg = "\n***** ERROR: writeCount option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
+ return false;
+ }
+ }
+ if (getWriteOverlap()) {
+
+ if (getWriteA()) {
+ _errorMsg = "\n***** ERROR: request either -wa for writeA OR -wo for writeOverlap, not both. *****";
+ return false;
+ } else if (getWriteB()) {
+ _errorMsg = "\n***** ERROR: request either -wb for writeB OR -wo for writeOverlap, not both. *****";
+ return false;
+ } else if (getWriteCount()) {
+ _errorMsg = "\n***** ERROR: request either -c for writeCount OR -wo for writeOverlap, not both. *****";
+ return false;
+ } else if (getAnyHit()) {
+ _errorMsg = "\n***** ERROR: request either -u for anyHit OR -wo for writeOverlap, not both. *****";
+ return false;
+ } else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
+ _errorMsg = "\n***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
+ return false;
+ }
+ }
+ if (getWriteB() || getLeftJoin()) {
+ if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
+ cerr << endl << "*****" << endl << "*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option." << endl << "*****" << endl;
+ }
+ }
+ if (getSameStrand() && getDiffStrand()) {
+ _errorMsg = "\n***** ERROR: request -s for sameStrand, or -S for diffStrand, not both. *****";
+ return false;
+ }
+
+ if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && getPrintHeader()) {
+ cerr << endl << "*****" << endl << "*****WARNING: -header option is not valid for BAM input." << endl << "*****" << endl;
+ setPrintHeader(false);
+ }
+ if (getAnyHit() || getNoHit() || getWriteCount()) {
+ setPrintable(false);
+ }
+ if (_files.size() != 2 ) {
+ return false;
+ }
+ return true;
+}
+
+bool ContextIntersect::determineOutputType() {
+ if (_outputTypeDetermined) {
+ return true;
+ }
+
+ //determine the maximum number of database fields.
+ for (int i=0; i < (int)_files.size(); i++) {
+ int numFields = _files[i]->getNumFields();
+ if ( numFields > _maxNumDatabaseFields) {
+ _maxNumDatabaseFields = numFields;
+ }
+ }
+
+ //If the query is BAM, and bed output wasn't specified, then the output is BAM.
+ if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
+ setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
+ _outputTypeDetermined = true;
+ return true;
+
+ }
+ return ContextBase::determineOutputType();
+
+}
+
+bool ContextIntersect::handle_a()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -a option given, but no query file specified. *****";
+ return false;
+ }
+
+ addInputFile(_argv[_i+1]);
+ _queryFileIdx = getNumInputFiles() -1;
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_abam()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -abam option given, but no query BAM file specified. *****";
+ return false;
+ }
+ addInputFile(_argv[_i+1]);
+ _queryFileIdx = getNumInputFiles() -1;
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_b()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -b option given, but no query file specified. *****";
+ return false;
+ }
+
+ addInputFile(_argv[_i+1]);
+ _databaseFileIdx = getNumInputFiles() -1;
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+
+
+bool ContextIntersect::handle_c()
+{
+ setWriteCount(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+
+bool ContextIntersect::handle_f()
+{
+ if ((_i+1) < _argc) {
+ setHaveFraction(true);
+ setOverlapFraction(atof(_argv[_i + 1]));
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+bool ContextIntersect::handle_loj()
+{
+ setLeftJoin(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_r()
+{
+ setReciprocal(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_s()
+{
+ setSameStrand(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_S()
+{
+ setDiffStrand(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_u()
+{
+ setAnyHit(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_v()
+{
+ setNoHit(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_wa()
+{
+ setWriteA(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_wao()
+{
+ setWriteAllOverlap(true);
+ setWriteOverlap(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_wb()
+{
+ setWriteB(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+bool ContextIntersect::handle_wo()
+{
+ setWriteOverlap(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
diff --git a/src/utils/Contexts/ContextIntersect.h b/src/utils/Contexts/ContextIntersect.h
new file mode 100644
index 0000000..0144a12
--- /dev/null
+++ b/src/utils/Contexts/ContextIntersect.h
@@ -0,0 +1,98 @@
+/*
+ * ContextIntersect.h
+ *
+ * Created on: Jan 6, 2014
+ * Author: nek3d
+ */
+
+#ifndef CONTEXTINTERSECT_H_
+#define CONTEXTINTERSECT_H_
+
+#include "ContextBase.h"
+
+class ContextIntersect : public ContextBase {
+public:
+ ContextIntersect();
+ virtual ~ContextIntersect();
+ virtual bool isValidState();
+
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+ virtual bool determineOutputType();
+
+ //NOTE: Query and database files will only be marked as such by either the
+ //parseCmdArgs method, or by explicitly setting them.
+ int getQueryFileIdx() const { return _queryFileIdx; }
+ void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
+ int getDatabaseFileIdx() const { return _databaseFileIdx; }
+ void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
+ const QuickString &getQueryFileName() const { return _files[_queryFileIdx]->getFileName(); }
+ const QuickString &getDatabaseFileName() const { return _files[_databaseFileIdx]->getFileName(); }
+ ContextFileType getQueryFileType() const { return _files[_queryFileIdx]->getFileType(); }
+ ContextFileType getDatabaseFileType() const { return _files[_databaseFileIdx]->getFileType(); }
+ ContextRecordType getQueryRecordType() const { return _files[_queryFileIdx]->getRecordType(); }
+ ContextRecordType getDatabaseRecordType() const { return _files[_databaseFileIdx]->getRecordType(); }
+ int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
+ void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
+
+ bool getAnyHit() const {return _anyHit; }
+ void setAnyHit(bool val) { _anyHit = val; }
+
+ bool getNoHit() const {return _noHit; }
+ void setNoHit(bool val) { _noHit = val; }
+
+ bool getLeftJoin() const {return _leftJoin; }
+ void setLeftJoin(bool val) { _leftJoin = val; }
+
+ bool getWriteA() const {return _writeA; }
+ void setWriteA(bool val) { _writeA = val; }
+
+ bool getWriteB() const {return _writeB; }
+ void setWriteB(bool val) { _writeB = val; }
+
+ bool getWriteCount() const {return _writeCount; }
+ void setWriteCount(bool val) { _writeCount = val; }
+
+ bool getWriteOverlap() const {return _writeOverlap; }
+ void setWriteOverlap(bool val) { _writeOverlap = val; }
+
+ bool getWriteAllOverlap() const {return _writeAllOverlap; }
+ void setWriteAllOverlap(bool val) { _writeAllOverlap = val; }
+
+ bool getHaveFraction() const {return _haveFraction; }
+ void setHaveFraction(bool val) { _haveFraction = val; }
+
+ float getOverlapFraction() const { return _overlapFraction; }
+ void setOverlapFraction(float fraction) { _overlapFraction = fraction; }
+
+ bool getReciprocal() const {return _reciprocal; }
+ void setReciprocal(bool val) { _reciprocal = val; }
+
+ bool getSameStrand() const {return _sameStrand; }
+ void setSameStrand(bool val) { _sameStrand = val; }
+ bool getForwardOnly() const { return _forwardOnly; }
+ bool getReverseOnly() const { return _reverseOnly; }
+
+ bool getDiffStrand() const {return _diffStrand; }
+ void setDiffStrand(bool val) { _diffStrand = val; }
+
+ virtual bool hasIntersectMethods() const { return true; }
+
+private:
+ virtual bool handle_a();
+ virtual bool handle_abam();
+ virtual bool handle_b();
+ virtual bool handle_c();
+ virtual bool handle_f();
+ virtual bool handle_loj();
+ virtual bool handle_r();
+ virtual bool handle_s();
+ virtual bool handle_S();
+ virtual bool handle_u();
+ virtual bool handle_v();
+ virtual bool handle_wa();
+ virtual bool handle_wao();
+ virtual bool handle_wb();
+ virtual bool handle_wo();
+};
+
+#endif /* CONTEXTINTERSECT_H_ */
diff --git a/src/utils/Contexts/ContextMap.cpp b/src/utils/Contexts/ContextMap.cpp
new file mode 100644
index 0000000..d94d088
--- /dev/null
+++ b/src/utils/Contexts/ContextMap.cpp
@@ -0,0 +1,118 @@
+/*
+ * ContextMap.cpp
+ *
+ * Created on: Jan 6, 2014
+ * Author: arq5x
+ */
+
+#include "ContextMap.h"
+
+ContextMap::ContextMap()
+{
+ // map requires sorted input
+ setSortedInput(true);
+ setLeftJoin(true);
+
+ // default to BED score column
+ setColumn(5);
+ // default to "sum"
+ setColumnOperation("sum");
+ // default to "." as a NULL value
+ setNullValue('.');
+}
+
+ContextMap::~ContextMap()
+{
+
+}
+
+
+bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ if (isUsed(_i - _skipFirstArgs)) {
+ continue;
+ }
+ else if (strcmp(_argv[_i], "-o") == 0) {
+ if (!handle_o()) return false;
+ }
+ else if (strcmp(_argv[_i], "-c") == 0) {
+ if (!handle_c()) return false;
+ }
+ else if (strcmp(_argv[_i], "-null") == 0) {
+ if (!handle_null()) return false;
+ }
+ }
+ return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
+}
+
+
+bool ContextMap::isValidState()
+{
+ if (!ContextIntersect::isValidState()) {
+ return false;
+ }
+
+ if (getDatabaseFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ //throw Error
+ cerr << endl << "*****"
+ << endl
+ << "***** ERROR: BAM database file not currently supported for the map tool."
+ << endl;
+ exit(1);
+ }
+ // TODO
+ // enforce any specific checks for Map.
+ return true;
+}
+
+
+// for map, -c is the column upon which to operate
+bool ContextMap::handle_c()
+{
+ if ((_i+1) < _argc) {
+ setColumn(atoi(_argv[_i + 1]));
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+
+// for map, -o is the operation to apply to the column (-c)
+bool ContextMap::handle_o()
+{
+ if ((_i+1) < _argc) {
+ setColumnOperation(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
+
+
+// for map, -null is a NULL vakue assigned
+// when no overlaps are detected.
+bool ContextMap::handle_null()
+{
+ if ((_i+1) < _argc) {
+ setNullValue(_argv[_i + 1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ }
+ return true;
+}
diff --git a/src/utils/Contexts/ContextMap.h b/src/utils/Contexts/ContextMap.h
new file mode 100644
index 0000000..b8ee57f
--- /dev/null
+++ b/src/utils/Contexts/ContextMap.h
@@ -0,0 +1,39 @@
+/*
+ * ContextMap.h
+ *
+ * Created on: Jan 7, 2014
+ * Author: arq5x
+ */
+
+#ifndef CONTEXTMAP_H_
+#define CONTEXTMAP_H_
+
+#include "ContextIntersect.h"
+
+class ContextMap : public ContextIntersect {
+public:
+ ContextMap();
+ virtual ~ContextMap();
+ virtual bool isValidState();
+
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+
+ int getColumn() const { return _column; }
+ void setColumn(int column) { _column = column; }
+
+ const QuickString & getColumnOperation() const { return _columnOperation; }
+ void setColumnOperation(const QuickString & operation) { _columnOperation = operation; }
+
+ const QuickString & getNullValue() const { return _nullValue; }
+ void setNullValue(const QuickString & nullValue) { _nullValue = nullValue; }
+
+ virtual bool hasIntersectMethods() const { return true; }
+
+private:
+ virtual bool handle_c();
+ virtual bool handle_o();
+ virtual bool handle_null();
+
+};
+
+#endif /* CONTEXTMAP_H_ */
diff --git a/src/utils/Contexts/ContextSample.cpp b/src/utils/Contexts/ContextSample.cpp
new file mode 100644
index 0000000..38fbcb3
--- /dev/null
+++ b/src/utils/Contexts/ContextSample.cpp
@@ -0,0 +1,79 @@
+/*
+ * ContextSample.cpp
+ *
+ * Created on: Jan 6, 2014
+ * Author: nek3d
+ */
+#include "ContextSample.h"
+
+ContextSample::ContextSample()
+{
+
+}
+
+ContextSample::~ContextSample()
+{
+
+}
+
+bool ContextSample::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
+ _argc = argc;
+ _argv = argv;
+ _skipFirstArgs = skipFirstArgs;
+ if (_argc < 2) {
+ setShowHelp(true);
+ return false;
+ }
+
+ setProgram(_programNames[argv[0]]);
+
+ _argsProcessed.resize(_argc - _skipFirstArgs, false);
+
+ for (_i=_skipFirstArgs; _i < argc; _i++) {
+ if (isUsed(_i - _skipFirstArgs)) {
+ continue;
+ }
+
+ else if (strcmp(_argv[_i], "-s") == 0) {
+ if (!handle_s()) return false;
+ }
+ }
+ return ContextBase::parseCmdArgs(argc, argv, _skipFirstArgs);
+}
+
+bool ContextSample::isValidState()
+{
+ if (!ContextBase::isValidState()) {
+ return false;
+ }
+ if (_files.size() != 1) {
+ _errorMsg = "\n***** ERROR: input file not specified. *****";
+ // Allow one and only input file for now
+ return false;
+ }
+ return true;
+}
+
+
+bool ContextSample::handle_s()
+{
+ _sameStrand = true;
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
+ return false;
+ }
+ if (strcmp(_argv[_i+1], "forward") == 0) {
+ _forwardOnly = true;
+ } else if (strcmp(_argv[_i+1], "reverse") == 0) {
+ _reverseOnly = true;
+ } else {
+ _errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
+ return false;
+ }
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
+
diff --git a/src/utils/Contexts/ContextSample.h b/src/utils/Contexts/ContextSample.h
new file mode 100644
index 0000000..2f4c1b4
--- /dev/null
+++ b/src/utils/Contexts/ContextSample.h
@@ -0,0 +1,31 @@
+/*
+ * ContextSample.h
+ *
+ * Created on: Jan 6, 2014
+ * Author: nek3d
+ */
+
+#ifndef CONTEXTSAMPLE_H_
+#define CONTEXTSAMPLE_H_
+
+#include "ContextBase.h"
+
+class ContextSample : public ContextBase {
+public:
+ ContextSample();
+ ~ContextSample();
+ bool isValidState();
+
+ virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
+
+ bool getSameStrand() const {return _sameStrand; }
+ void setSameStrand(bool val) { _sameStrand = val; }
+ bool getForwardOnly() const { return _forwardOnly; }
+ bool getReverseOnly() const { return _reverseOnly; }
+
+private:
+ virtual bool handle_s();
+};
+
+
+#endif /* CONTEXTSAMPLE_H_ */
diff --git a/src/utils/Contexts/Makefile b/src/utils/Contexts/Makefile
new file mode 100644
index 0000000..7ddc3c6
--- /dev/null
+++ b/src/utils/Contexts/Makefile
@@ -0,0 +1,42 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= ContextBase.cpp ContextBase.h ContextIntersect.cpp ContextIntersect.h ContextMap.cpp ContextMap.h ContextSample.cpp ContextSample.h
+OBJECTS= ContextBase.o ContextIntersect.o ContextMap.o ContextSample.o
+_EXT_OBJECTS=ParseTools.o QuickString.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)/ContextBase.o \
+ $(OBJ_DIR)/ContextIntersect.o \
+ $(OBJ_DIR)/ContextMap.o \
+ $(OBJ_DIR)/ContextSample.o
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/Fasta/Fasta.cpp b/src/utils/Fasta/Fasta.cpp
index bedf311..076f06d 100644
--- a/src/utils/Fasta/Fasta.cpp
+++ b/src/utils/Fasta/Fasta.cpp
@@ -8,12 +8,13 @@
#include "Fasta.h"
-FastaIndexEntry::FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len)
+FastaIndexEntry::FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len, bool useFullHeader)
: name(name)
, length(length)
, offset(offset)
, line_blen(line_blen)
, line_len(line_len)
+ , useFullHeader(useFullHeader)
{}
FastaIndexEntry::FastaIndexEntry(void) // empty constructor
@@ -30,16 +31,19 @@ void FastaIndexEntry::clear(void)
// check if we have already recorded a real offset
line_blen = NULL;
line_len = NULL;
+ useFullHeader = false;
}
ostream& operator<<(ostream& output, const FastaIndexEntry& e) {
// just write the first component of the name, for compliance with other tools
- output << split(e.name, ' ').at(0) << "\t" << e.length << "\t" << e.offset << "\t" <<
- e.line_blen << "\t" << e.line_len;
+ output << (e.useFullHeader? e.name : split(e.name, ' ').at(0))
+ << "\t" << e.length << "\t" << e.offset << "\t"
+ << e.line_blen << "\t" << e.line_len;
return output; // for multiple << operators.
}
-FastaIndex::FastaIndex(void)
+FastaIndex::FastaIndex(bool useFullHeader)
+ : useFullHeader(useFullHeader)
{}
void FastaIndex::readIndexFile(string fname) {
@@ -55,12 +59,14 @@ void FastaIndex::readIndexFile(string fname) {
if (fields.size() == 5) { // if we don't get enough fields then there is a problem with the file
// note that fields[0] is the sequence name
char* end;
- string name = split(fields[0], " \t").at(0); // key by first token of name
+ string name = useFullHeader ? fields[0] :
+ split(fields[0], " \t").at(0); // key by first token of name
sequenceNames.push_back(name);
this->insert(make_pair(name, FastaIndexEntry(fields[0], atoi(fields[1].c_str()),
- strtoll(fields[2].c_str(), &end, 10),
- atoi(fields[3].c_str()),
- atoi(fields[4].c_str()))));
+ strtoll(fields[2].c_str(), &end, 10),
+ atoi(fields[3].c_str()),
+ atoi(fields[4].c_str()),
+ useFullHeader)));
} else {
cerr << "Warning: malformed fasta index file " << fname <<
"does not have enough fields @ line " << linenum << endl;
@@ -181,12 +187,13 @@ void FastaIndex::indexReference(string refname) {
}
void FastaIndex::flushEntryToIndex(FastaIndexEntry& entry) {
- string name = split(entry.name, " \t").at(0); // key by first token of name
+ string name = useFullHeader? entry.name :
+ split(entry.name, " \t").at(0); // key by first token of name
sequenceNames.push_back(name);
this->insert(make_pair(name, FastaIndexEntry(entry.name, entry.length,
- entry.offset, entry.line_blen,
- entry.line_len)));
-
+ entry.offset, entry.line_blen,
+ entry.line_len,
+ useFullHeader)));
}
void FastaIndex::writeIndexFile(string fname) {
@@ -225,13 +232,15 @@ bool FastaIndex::chromFound(string name) {
string FastaIndex::indexFileExtension() { return ".fai"; }
-void FastaReference::open(string reffilename, bool usemmap) {
+void FastaReference::open(string reffilename, bool usemmap, bool useFullHeader) {
filename = reffilename;
if (!(file = fopen(filename.c_str(), "r"))) {
cerr << "could not open " << filename << endl;
exit(1);
}
- index = new FastaIndex();
+ if (useFullHeader)
+ usingfullheader = true;
+ index = new FastaIndex(useFullHeader);
struct stat stFileInfo;
string indexFileName = filename + index->indexFileExtension();
// if we can find an index file, use it
diff --git a/src/utils/Fasta/Fasta.h b/src/utils/Fasta/Fasta.h
index 68a8bf8..f9d2820 100644
--- a/src/utils/Fasta/Fasta.h
+++ b/src/utils/Fasta/Fasta.h
@@ -29,7 +29,8 @@ using namespace std;
class FastaIndexEntry {
friend ostream& operator<<(ostream& output, const FastaIndexEntry& e);
public:
- FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len);
+ FastaIndexEntry(string name, int length, long long offset,
+ int line_blen, int line_len, bool useFullHeader);
FastaIndexEntry(void);
~FastaIndexEntry(void);
string name; // sequence name
@@ -37,14 +38,16 @@ class FastaIndexEntry {
long long offset; // bytes offset of sequence from start of file
int line_blen; // line length in bytes, sequence characters
int line_len; // line length including newline
+ bool useFullHeader;
void clear(void);
};
class FastaIndex : public map<string, FastaIndexEntry> {
friend ostream& operator<<(ostream& output, FastaIndex& i);
public:
- FastaIndex(void);
+ FastaIndex(bool useFullHeader);
~FastaIndex(void);
+ bool useFullHeader;
vector<string> sequenceNames;
void indexReference(string refName);
void readIndexFile(string fname);
@@ -58,10 +61,12 @@ class FastaIndex : public map<string, FastaIndexEntry> {
class FastaReference {
public:
- void open(string reffilename, bool usemmap = false);
+ void open(string reffilename, bool usemmap = false,
+ bool useFullHeader = false);
bool usingmmap;
string filename;
- FastaReference(void) : usingmmap(false) { }
+ bool usingfullheader;
+ FastaReference(void) : usingmmap(false), usingfullheader(false) { }
~FastaReference(void);
FILE* file;
void* filemm;
diff --git a/src/utils/Fasta/Makefile b/src/utils/Fasta/Makefile
index 17bfdf6..de687c1 100644
--- a/src/utils/Fasta/Makefile
+++ b/src/utils/Fasta/Makefile
@@ -10,7 +10,7 @@ INCLUDES =
# define our source and object files
# ----------------------------------
SOURCES= Fasta.cpp Fasta.h split.cpp split.h
-OBJECTS= $(SOURCES:.cpp=.o)
+OBJECTS= Fasta.o split.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
diff --git a/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp b/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
new file mode 100644
index 0000000..ab717f9
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
@@ -0,0 +1,100 @@
+#include "BamFileReader.h"
+#include "ParseTools.h"
+#include <cstdio>
+BamFileReader::BamFileReader()
+: _bamReader(NULL),
+ _eof(false),
+ _useTags(true)
+{
+
+}
+
+BamFileReader::~BamFileReader()
+{
+}
+
+bool BamFileReader::open()
+{
+ _bamHeader = _bamReader->GetHeaderText();
+ _references = _bamReader->GetReferenceData();
+
+ return true;
+}
+
+bool BamFileReader::isOpen() const
+{
+ return _bamReader->IsOpen();
+}
+
+void BamFileReader::close()
+{
+// _bamReader->Close();
+}
+
+bool BamFileReader::readEntry()
+{
+ if (_useTags) {
+ if (_bamReader->GetNextAlignment(_bamAlignment)) {
+ return true;
+ }
+ } else {
+ if (_bamReader->GetNextAlignmentCore(_bamAlignment)) {
+ return true;
+ }
+ }
+ //hit end of file
+ _eof = true;
+ return false;
+}
+
+void BamFileReader::getChrName(QuickString &str) const
+{
+ int refId = _bamAlignment.RefID;
+ if (refId < 0) {
+ return;
+ }
+ str = _references[refId].RefName;
+}
+
+int BamFileReader::getBamChrId() const
+{
+ return _bamAlignment.RefID;
+}
+
+int BamFileReader::getStartPos() const
+{
+ return _bamAlignment.Position;
+}
+
+int BamFileReader::getEndPos() const
+{
+ return _bamAlignment.GetEndPosition(false, false);
+}
+
+void BamFileReader::getName(QuickString &str) const
+{
+ if (!_useTags) {
+ str = _bamAlignment.SupportData.AllCharData.c_str();
+ } else {
+ str = _bamAlignment.Name;
+ }
+ if (_bamAlignment.IsFirstMate()) {
+ str += "/1";
+ }
+ else if (_bamAlignment.IsSecondMate()) {
+ str += "/2";
+ }
+}
+
+void BamFileReader::getScore(QuickString &str) const
+{
+ int2str(_bamAlignment.MapQuality, str);
+}
+
+char BamFileReader::getStrand() const
+{
+ if (_bamAlignment.IsReverseStrand()) {
+ return '-';
+ }
+ return '+';
+}
diff --git a/src/utils/FileRecordTools/FileReaders/BamFileReader.h b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
new file mode 100644
index 0000000..8bea945
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
@@ -0,0 +1,67 @@
+/*
+ * BamFileReader.h
+ *
+ * Created on: Dec 4, 2012
+ * Author: nek3d
+ */
+
+#ifndef BAMFILEREADER_H_
+#define BAMFILEREADER_H_
+
+using namespace std;
+
+#include "FileReader.h"
+#include "QuickString.h"
+#include "api/BamReader.h"
+#include "api/BamAux.h"
+
+class BamFileReader : public FileReader {
+public:
+ BamFileReader();
+ virtual ~BamFileReader();
+ virtual bool open(); //open the file
+ virtual bool isOpen() const;
+ virtual void close();
+ virtual bool eof() const {
+ return _eof;
+ }
+
+ //setUseTags will tell the BamReader to give us all
+ //the extra tag information in a BAM record. By default,
+ //this is set to false, so not using them, which reduces
+ //the run time of reading a BAM file by more than half.
+ virtual void setUseTags(bool flag) { _useTags = flag; }
+ void setBamReader(BamTools::BamReader *bamReader) { _bamReader = bamReader; }
+ virtual bool readEntry();
+
+ virtual bool hasHeader() const { return _bamReader->IsOpen(); } //any open Bam file automatically has a header
+ virtual const QuickString &getHeader() const { return _bamHeader; }
+ const BamTools::RefVector &getReferences() const { return _references; }
+
+ const BamTools::BamAlignment &getAlignment() const { return _bamAlignment; }
+
+
+ void getChrName(QuickString &) const;
+ int getBamChrId() const;
+ int getStartPos() const;
+ int getEndPos() const;
+ void getName(QuickString &) const;
+ void getScore(QuickString &) const;
+ char getStrand() const;
+ virtual int getNumFields() const { return MINIMUM_PRINTABLE_BAM_FIELDS; }
+
+protected:
+
+ BamTools::BamReader *_bamReader;
+ BamTools::BamAlignment _bamAlignment;
+ bool _eof;
+ QuickString _bamHeader;
+ BamTools::RefVector _references;
+ bool _useTags;
+
+ static const int MINIMUM_PRINTABLE_BAM_FIELDS = 6;
+ void extractNameFromCore();
+};
+
+
+#endif /* BAMFILEREADER_H_ */
diff --git a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
new file mode 100644
index 0000000..27f0789
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
@@ -0,0 +1,132 @@
+/*
+ * BufferedStreamMgr.cpp
+ *
+ * Created on: Jul 9, 2013
+ * Author: nek3d
+ */
+
+#include "BufferedStreamMgr.h"
+#include "CompressionTools.h"
+#include "InputStreamMgr.h"
+#include <fstream>
+
+BufferedStreamMgr::BufferedStreamMgr(const QuickString &filename)
+: _inputStreamMgr(NULL),
+ _mainBuf(NULL),
+ _filename(filename),
+ _mainBufCurrStartPos(0),
+ _mainBufCurrLen(0),
+ _eof(false),
+ _useBufSize(0),
+ _streamFinished(false)
+{
+
+}
+
+BufferedStreamMgr::~BufferedStreamMgr()
+{
+
+ delete [] _mainBuf;
+ _mainBuf = NULL;
+
+ delete _inputStreamMgr;
+ _inputStreamMgr = NULL;
+}
+
+bool BufferedStreamMgr::init()
+{
+ _inputStreamMgr = new InputStreamMgr(_filename);
+ if (!_inputStreamMgr->init()) {
+ return false;
+ }
+ if (_inputStreamMgr->isBam()) {
+ //there is a special check for a BAM file's magic string inside
+ //the inputStreamMgr's init method. If it is found, we can
+ //stop here.
+ _typeChecker.setBam();
+ return true;
+ }
+ if (!getTypeData()) {
+ return false;
+ }
+ if (_inputStreamMgr->isGzipped()) {
+ _useBufSize = GZIP_LINE_BUF_SIZE;
+ } else {
+ _useBufSize = MAIN_BUF_READ_SIZE;
+ }
+
+ size_t trueBufSize = max(_useBufSize, (int)_currScanBuffer.size());
+ _useBufSize = trueBufSize;
+ _mainBuf = new bufType[_useBufSize +1];
+ memset(_mainBuf, 0, _useBufSize +1);
+ memcpy(_mainBuf, _currScanBuffer.c_str(), _currScanBuffer.size());
+ _mainBufCurrLen = _currScanBuffer.size();
+
+ return true;
+}
+
+bool BufferedStreamMgr::getTypeData()
+{
+ _currScanBuffer = _inputStreamMgr->getSavedData();
+ _typeChecker.setFilename(_filename);
+ do {
+ if (!_typeChecker.scanBuffer(_currScanBuffer.c_str(), _currScanBuffer.size()) && !_typeChecker.needsMoreData()) {
+ return false;
+ } else if (_typeChecker.needsMoreData()) {
+ _inputStreamMgr->populateScanBuffer();
+ _currScanBuffer.append(_inputStreamMgr->getSavedData());
+ }
+ } while (_typeChecker.needsMoreData());
+ if (_inputStreamMgr->resetStream()) {
+ _currScanBuffer.clear();
+ }
+ return true;
+}
+
+bool BufferedStreamMgr::getLine(QuickString &line)
+{
+ line.clear();
+
+ if (_mainBufCurrStartPos >= _mainBufCurrLen) {
+ if (!readFileChunk()) {
+ _eof = true;
+ return false;
+ }
+ }
+ while (1) {
+ int searchPos = _mainBufCurrStartPos;
+ while (searchPos < _mainBufCurrLen && _mainBuf[searchPos] != '\n') {
+ searchPos++;
+ }
+
+ line.append((char *)_mainBuf + _mainBufCurrStartPos, searchPos - _mainBufCurrStartPos);
+ _mainBufCurrStartPos = searchPos +1;
+ if (searchPos == _mainBufCurrLen) { //hit end of buffer, but no newline yet
+ if (!readFileChunk()) { //hit eof
+ return true;
+ }
+ } else if (_mainBuf[searchPos] == '\n') {
+ return true;
+ }
+ }
+}
+
+bool BufferedStreamMgr::readFileChunk()
+{
+ if (eof()) {
+ return false;
+ }
+ memset(_mainBuf, 0, _useBufSize +1);
+ _mainBufCurrStartPos = 0;
+
+ if (!_streamFinished) {
+ _mainBufCurrLen = _inputStreamMgr->read((char *)_mainBuf, _useBufSize);
+ if (_mainBufCurrLen < _useBufSize) {
+ _streamFinished = true;
+ }
+ return _mainBufCurrLen > 0;
+ } else {
+ _mainBufCurrLen = 0;
+ return false;
+ }
+}
diff --git a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
new file mode 100644
index 0000000..2a77854
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
@@ -0,0 +1,53 @@
+/*
+ * BufferedStreamMgr.h
+ *
+ * Created on: Jul 9, 2013
+ * Author: nek3d
+ */
+
+#ifndef BUFFEREDSTREAMMGR_H_
+#define BUFFEREDSTREAMMGR_H_
+
+using namespace std;
+
+#include <iostream>
+#include "QuickString.h"
+#include "FileRecordTypeChecker.h"
+#include "InputStreamMgr.h"
+
+class BufferedStreamMgr {
+public:
+ BufferedStreamMgr(const QuickString &filename);
+ ~BufferedStreamMgr();
+
+ bool init();
+
+ const FileRecordTypeChecker & getTypeChecker() const { return _typeChecker; }
+
+ bool eof() const { return _eof; }
+ bool getLine(QuickString &line);
+ BamTools::BamReader *getBamReader() { return _inputStreamMgr->getBamReader(); }
+
+private:
+ InputStreamMgr *_inputStreamMgr;
+ typedef unsigned char bufType;
+ bufType *_mainBuf;
+
+ FileRecordTypeChecker _typeChecker;
+ QuickString _filename;
+
+ int _mainBufCurrStartPos;
+ int _mainBufCurrLen;
+ bool _eof;
+ int _useBufSize;
+ bool _streamFinished;
+ QuickString _currScanBuffer;
+ //The minus ones in these constants are for leaving room for a null terminator after reading into buffers.
+ static const int MAIN_BUF_READ_SIZE = 1023; // 2 Kb minus 1
+ static const int GZIP_LINE_BUF_SIZE = 8191; // 8K
+ bool readFileChunk();
+ bool getTypeData();
+};
+
+
+#endif /* BUFFEREDSTREAMMGR_H_ */
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.cpp b/src/utils/FileRecordTools/FileReaders/FileReader.cpp
new file mode 100644
index 0000000..967b82a
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.cpp
@@ -0,0 +1,33 @@
+#include <iostream>
+#include <cstring>
+#include "FileReader.h"
+#include "BufferedStreamMgr.h"
+
+FileReader::FileReader()
+:
+ _bufStreamMgr(NULL),
+ _isFileOpen(false),
+ _currChromId(-1)
+{
+}
+
+FileReader::~FileReader() {
+}
+
+bool FileReader::open() {
+
+ if (_isFileOpen) {
+ return true;
+ } else {
+ fprintf(stderr, "Error: bad input stream.\n");
+ exit(1);
+ }
+ return false; //can't reach this point, but it's here to satisfy the compiler.
+}
+
+void FileReader::close() {
+}
+
+bool FileReader::eof() const {
+ return _bufStreamMgr->eof();
+}
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.h b/src/utils/FileRecordTools/FileReaders/FileReader.h
new file mode 100644
index 0000000..29c2563
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.h
@@ -0,0 +1,42 @@
+#ifndef FILEREADER_H_
+#define FILEREADER_H_
+
+using namespace std;
+
+#include <string>
+#include <fstream>
+#include <map>
+#include "QuickString.h"
+//#include "ContextBase.h"
+
+#include "BufferedStreamMgr.h"
+
+class FileReader {
+public:
+ FileReader();
+ virtual ~FileReader();
+ void setFileName(const string &filename) { _filename = filename; }
+ void setInputStream(BufferedStreamMgr *bufStreamMgr) {
+ _bufStreamMgr = bufStreamMgr;
+ _isFileOpen = true;
+
+ }
+ virtual bool open(); //open the file
+ virtual bool isOpen() const { return _isFileOpen; }
+ virtual void close();
+ virtual bool eof() const;
+ virtual bool readEntry() =0; // this is an abstract base class.
+ virtual int getCurrChromdId() const { return _currChromId; }
+ virtual bool hasHeader() const = 0;
+ virtual const QuickString &getHeader() const =0;
+ virtual int getNumFields() const = 0;
+protected:
+ string _filename;
+ BufferedStreamMgr *_bufStreamMgr;
+
+ bool _isFileOpen;
+ int _currChromId;
+
+};
+
+#endif // FILEREADER_H_
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
new file mode 100644
index 0000000..2035b9c
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
@@ -0,0 +1,269 @@
+/*
+ * InputStreamMgr.cpp
+ *
+ * Created on: Mar 21, 2013
+ * Author: nek3d
+ */
+
+#include "InputStreamMgr.h"
+#include <cstring> //for memset
+#include "gzstream.h"
+#include "CompressionTools.h"
+
+const char *InputStreamMgr::FIFO_STRING_LITERAL = "/dev/fd";
+
+InputStreamMgr::InputStreamMgr(const QuickString &filename, bool buildScanBuffer)
+:
+ _filename(filename),
+ _pushBackStreamBuf(NULL),
+ _inputFileStream(NULL),
+ _infStreamBuf(NULL),
+ _oldInputStream(NULL),
+ _isStdin(false),
+ _isGzipped(false),
+ _isBam(false),
+ _isBgzipped(false),
+ _tmpZipBuf(NULL),
+ _bamRuledOut(false),
+ _streamFinished(false),
+ _numBytesInBuffer(0),
+ _bamReader(NULL),
+ _bgStream(NULL)
+{
+ _possibleBamCode.resize(4, 0);
+}
+
+
+InputStreamMgr::~InputStreamMgr() {
+ delete _pushBackStreamBuf;
+ _pushBackStreamBuf = NULL;
+
+ delete _inputFileStream;
+ _inputFileStream = NULL;
+
+ delete _oldInputStream;
+ _oldInputStream = NULL;
+
+ delete _infStreamBuf;
+ _infStreamBuf = NULL;
+
+ delete _bamReader;
+ _bgStream = NULL;
+
+ delete _bgStream;
+ _bgStream = NULL;
+
+ delete _finalInputStream;
+ _finalInputStream = NULL;
+
+ delete [] _tmpZipBuf;
+ _tmpZipBuf = NULL;
+}
+
+bool InputStreamMgr::init()
+{
+ if (_filename == "-" || _filename == "stdin") { //stdin
+ _isStdin = true;
+ //peek at the first char of stdin to see if this is gzipped.
+ if ((unsigned char)cin.peek() == 0x1f) {
+ _isGzipped = true;
+ }
+ _pushBackStreamBuf = new PushBackStreamBuf(cin.rdbuf());
+ } else {
+ if (strncmp(_filename.c_str(), FIFO_STRING_LITERAL, strlen(FIFO_STRING_LITERAL)) == 0) {
+ _isStdin = true;
+ }
+ _inputFileStream = new ifstream(_filename.c_str());
+ if (_inputFileStream->fail()) {
+ cerr << "Error: Unable to open file " << _filename << ". Exiting." << endl;
+ delete _inputFileStream;
+ _inputFileStream = NULL;
+ exit(1);
+ }
+ //peek at the first char of stdin to see if this is gzipped.
+ if ((unsigned char)_inputFileStream->peek() == 0x1f) {
+ _isGzipped = true;
+ }
+ _pushBackStreamBuf = new PushBackStreamBuf(_inputFileStream->rdbuf());
+ }
+ //now we have a PushBackStreamBuf. Make a new stream.
+ _finalInputStream = new istream(_pushBackStreamBuf);
+ populateScanBuffer();
+ return true;
+}
+
+int InputStreamMgr::read(char *data, size_t dataSize)
+{
+ size_t origRead = 0;
+ if (!_saveDataStr.empty()) {
+ //must first copy contents of savedData into requested data read buffer.
+ if (dataSize >= _saveDataStr.size()) {
+ //They asked for the same amount of data or more than we saved. Give them all the saved data,
+ //then decrement the requested data size accordingly.
+ origRead = _saveDataStr.size();
+ memcpy(data, _saveDataStr.c_str(), origRead);
+ data += origRead;
+ dataSize -= origRead;
+ _saveDataStr.clear();
+ } else {
+ //This part is tricky. They want less data than we saved. Give them what they
+ //requested, then delete from the front of the saveDataStr by using it's substr method.
+ memcpy(data, _saveDataStr.c_str(), dataSize);
+ QuickString newDataStr;
+ _saveDataStr.substr(newDataStr, dataSize, _saveDataStr.size() - dataSize);
+ _saveDataStr = newDataStr;
+ return dataSize;
+ }
+ }
+ if (_streamFinished) {
+ return origRead;
+ }
+ if (_isBgzipped) {
+ return (int)(origRead + _bgStream->Read(data, dataSize));
+ }
+ _finalInputStream->read(data, dataSize);
+ return origRead + _finalInputStream->gcount();
+}
+
+void InputStreamMgr::populateScanBuffer()
+{
+ _scanBuffer.clear();
+ _saveDataStr.clear();
+ int numChars=0;
+ int currChar = 0;
+ while (1) {
+ if (_isGzipped && _bamRuledOut) {
+ readZipChunk();
+ return;
+ }
+ currChar = _pushBackStreamBuf->sbumpc();
+ //Stop when EOF hit.
+ if (currChar == EOF) {
+ break;
+ }
+ numChars++;
+ _scanBuffer.push_back(currChar);
+ if (_isGzipped) {
+ if (!_bamRuledOut && detectBamOrBgzip(numChars, currChar)) {
+ return;
+ }
+ if (numChars == 0) {
+ continue; //this will only happen when we've just discovered that this
+ //is definitely not BAM, and want to start over.
+ }
+ }
+
+ //Stop if we have the minimum number of bytes and newline is hit.
+ //For gzip, stop at SCAN_BUFFER_SIZE.
+ if (currChar == '\n' && numChars >= MIN_SCAN_BUFFER_SIZE ){
+ break;
+ }
+ }
+ _numBytesInBuffer = _scanBuffer.size();
+
+ //append it to the savedDataStr.
+ _scanBuffer.toStr(_saveDataStr, true);
+}
+
+bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
+{
+ //Look for the BAM magic string "BAM\1" in the first fouur characters of the input stream.
+ //In compressed form, the first char is the gzip signifier, which was already found.
+ //The next three are the integers 139, 8, and 4.
+ if (numChars < 5) {
+ _possibleBamCode[numChars -1] = currChar;
+ //special: test for BAM
+ if (numChars == 4 && _possibleBamCode[1] == 139 && _possibleBamCode[2] == 8 && _possibleBamCode[3] == 4) {
+ //BAM magic string detected.This is either a BAM or bgzip file. To find out which, we have to try and
+ //open the file as BAM, with a BAM reader, and see if the header and references are both non-empty.
+ //However, if they are empty, we will have had to save all bytes consumed in the attempt, meaning still
+ //fill the scanBuffer and push it back onto the pushBackStream as normal.
+ for (; numChars < BAM_SCAN_BUFFER_SIZE; numChars++) {
+ currChar = _pushBackStreamBuf->sbumpc();
+ //Stop when EOF hit.
+ if (currChar == EOF) {
+ break;
+ }
+ _scanBuffer.push_back(currChar);
+
+ }
+ _pushBackStreamBuf->pushBack(_scanBuffer);
+
+ //ok, now all the data read so far is saved in the scan buffer, and pushbackstream is reset.
+ //now we make a BamReader and try to open the file.
+
+
+ _bamReader = new BamTools::BamReader();
+ if (!_bamReader->OpenStream(_finalInputStream)) {
+ //This is NOT a bam file, but it is bgzipped.
+ _pushBackStreamBuf->clear();
+ //Put all bytes read so far back onto the scan buffer, then reset
+ //everything so that we're effectively starting over.
+ _pushBackStreamBuf->pushBack(_scanBuffer);
+ _scanBuffer.clear();
+ numChars = 0;
+ _isBam = false;
+ _isBgzipped = true;
+ _bamRuledOut = true;
+ _numBytesInBuffer = 0;
+ delete _bamReader;
+ _bamReader = NULL;
+
+ //Alter the finalInputSream to become a bgzfReader.
+ _bgStream = new BamTools::Internal::BgzfStream();
+ _bgStream->OpenStream(_finalInputStream, BamTools::IBamIODevice::ReadOnly);
+
+ return false;
+ }
+ //This is a BAM file.
+ _isBam = true;
+ _numBytesInBuffer = _scanBuffer.size();
+ return true;
+ } else if (numChars == 4) {
+ //This is a gzipped file, and it is not bgzipped or BAM.
+ _pushBackStreamBuf->clear();
+ _pushBackStreamBuf->pushBack(_scanBuffer);
+ _scanBuffer.clear();
+ numChars = 0;
+ _isBam = false;
+ _isBgzipped = false;
+ _bamRuledOut = true;
+ _numBytesInBuffer = 0;
+ _infStreamBuf = new InflateStreamBuf(_finalInputStream);
+ delete _oldInputStream;
+ _oldInputStream = _finalInputStream;
+ _finalInputStream = new istream(_infStreamBuf);
+ return false;
+ }
+ }
+ return false;
+}
+
+void InputStreamMgr::readZipChunk()
+{
+ if (_tmpZipBuf == NULL) {
+ _tmpZipBuf = new char[SCAN_BUFFER_SIZE +1];
+ }
+ memset(_tmpZipBuf, 0, SCAN_BUFFER_SIZE +1);
+ size_t numCharsRead = read(_tmpZipBuf, (size_t)SCAN_BUFFER_SIZE);
+ _saveDataStr.append(_tmpZipBuf);
+ _numBytesInBuffer = _saveDataStr.size();
+ if ((int)numCharsRead < SCAN_BUFFER_SIZE) {
+ _streamFinished = true;
+ }
+ return;
+}
+
+bool InputStreamMgr::resetStream()
+{
+ _saveDataStr.clear();
+ if (!_isBam && !_isStdin && !_isGzipped) {
+ //For non-compressed, non-stdin file input, just re-open the file.
+ delete _finalInputStream;
+ _finalInputStream = new ifstream(_filename.c_str());
+ return true;
+ }
+ return false;
+}
+
+
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
new file mode 100644
index 0000000..1c463d3
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
@@ -0,0 +1,74 @@
+/*
+ * InputStreamMgr.h
+ *
+ * Created on: Mar 21, 2013
+ * Author: nek3d
+ */
+
+#ifndef INPUTSTREAMMGR_H_
+#define INPUTSTREAMMGR_H_
+
+using namespace std;
+
+#include "PushBackStreamBuf.h"
+#include "InflateStreamBuf.h"
+#include "QuickString.h"
+#include "api/BamReader.h"
+#include "api/internal/io/BgzfStream_p.h"
+
+#include <iostream>
+
+class InputStreamMgr {
+public:
+ //Contsructor: 1st arg can be "-" for stdin. set 2nd arg false if fileType already known.
+ InputStreamMgr(const QuickString &filename, bool buildScanBuffer = true);
+ ~InputStreamMgr();
+ bool init();
+ int read(char *data, size_t dataSize);
+
+ //use getScanBuffer for auto-detection of file types.
+// istream *getFinalStream() { return _finalInputStream; }
+ const BTlist<int> &getScanBuffer() const { return _scanBuffer; }
+ int getBufferLength() const { return _numBytesInBuffer; }
+ void populateScanBuffer();
+ const QuickString &getSavedData() const { return _saveDataStr; }
+ bool isGzipped() const { return _isGzipped; }
+ PushBackStreamBuf *getPushBackStreamBuf() const {return _pushBackStreamBuf; }
+// void getSavedData(QuickString &str) const { str = _saveDataStr; }
+ bool isBam() const { return _isBam; }
+ BamTools::BamReader *getBamReader() { return _bamReader; }
+ bool resetStream();
+
+
+private:
+ QuickString _filename;
+ PushBackStreamBuf *_pushBackStreamBuf;
+ ifstream *_inputFileStream;
+ BTlist<int> _scanBuffer;
+ QuickString _saveDataStr;
+ InflateStreamBuf *_infStreamBuf;
+ istream * _finalInputStream;
+ istream *_oldInputStream;
+ bool _isStdin;
+ bool _isGzipped;
+ bool _isBam;
+ bool _isBgzipped;
+ char *_tmpZipBuf;
+ bool _bamRuledOut;
+ bool _streamFinished;
+ vector<int> _possibleBamCode;
+ static const int SCAN_BUFFER_SIZE = 4096; // 4 K buffer
+ static const int BAM_SCAN_BUFFER_SIZE = 32768; // 32K
+ static const int MIN_SCAN_BUFFER_SIZE = 2048;
+ int _numBytesInBuffer; //this will hold the length of the buffer after the scan.
+ BamTools::BamReader *_bamReader;
+ BamTools::Internal::BgzfStream *_bgStream;
+
+ static const char *FIFO_STRING_LITERAL;
+ void readZipChunk();
+ bool detectBamOrBgzip(int &numChars, int currChar);
+// void decompressBuffer();
+
+};
+
+#endif /* INPUTSTREAMMGR_H_ */
diff --git a/src/utils/FileRecordTools/FileReaders/Makefile b/src/utils/FileRecordTools/FileReaders/Makefile
new file mode 100644
index 0000000..37ff6e8
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/Makefile
@@ -0,0 +1,41 @@
+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/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
new file mode 100644
index 0000000..38074ed
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
@@ -0,0 +1,135 @@
+#include "SingleLineDelimTextFileReader.h"
+#include <iostream>
+#include "BufferedStreamMgr.h"
+#include "ParseTools.h"
+
+SingleLineDelimTextFileReader::SingleLineDelimTextFileReader(int numFields, char delimChar)
+: _numFields(numFields),
+ _delimChar(delimChar),
+ _fullHeaderFound(false),
+ _currDataPos(0),
+ _lineNum(0)
+{
+ _delimPositions = new int[numFields +1];
+}
+
+SingleLineDelimTextFileReader::~SingleLineDelimTextFileReader()
+{
+ delete [] _delimPositions;
+ _delimPositions = NULL;
+}
+
+bool SingleLineDelimTextFileReader::readEntry()
+{
+ if (!_isFileOpen) {
+ return false;
+ }
+
+ if (_bufStreamMgr->eof()) {
+ return false;
+ }
+ if (!_bufStreamMgr->getLine(_sLine)) {
+ return false;
+ }
+ _lineNum++;
+ if (_sLine.empty()) {
+ return false;
+ }
+
+ //scan the whole header in one call.
+ bool wasHeader = false;
+ while (detectAndHandleHeader()) { //header line
+ if (!_bufStreamMgr->getLine(_sLine)) {
+ return false;
+ _lineNum++;
+ }
+ }
+ //after the first time we find a header, any other header line
+ //doesn't count, and should not be added to the header, because it is a
+ // "commented out record."
+ _fullHeaderFound = true;
+
+ //check to make sure line has something besides whitespace.
+ bool hasNonSpace = false;
+ int lineLen = _sLine.size();
+ for (int i=0; i < lineLen; i++) {
+ if (!isspace(_sLine[i])) {
+ hasNonSpace = true;
+ break;
+ }
+ }
+ if (!hasNonSpace) {
+ return false;
+ }
+
+ //trim off any white space from end of line.
+ int currPos = lineLen-1;
+ while (isspace(_sLine[currPos])) {
+ currPos--;
+ }
+ _sLine.resize(currPos +1);
+
+ if (wasHeader) {
+ return true;
+ }
+
+ if (!findDelimiters()) {
+ return false;
+ }
+ return true;
+}
+
+
+void SingleLineDelimTextFileReader::getField(int fieldNum, QuickString &str) const {
+ int startPos = _delimPositions[fieldNum] +1;
+ int endPos = _delimPositions[fieldNum+1];
+ str.assign(_sLine.c_str() + startPos, endPos - startPos);
+}
+
+
+void SingleLineDelimTextFileReader::getField(int fieldNum, int &val) {
+ getField(fieldNum, _tempChrPosStr);
+ val = str2chrPos(_tempChrPosStr.c_str());
+}
+
+void SingleLineDelimTextFileReader::getField(int fieldNum, char &val) const {
+ val = _sLine[_delimPositions[fieldNum] +1];
+}
+
+void SingleLineDelimTextFileReader::appendField(int fieldNum, QuickString &str) const {
+ int startPos = _delimPositions[fieldNum] +1;
+ int endPos = _delimPositions[fieldNum+1];
+ str.append(_sLine.c_str() + startPos, endPos - startPos);
+}
+
+bool SingleLineDelimTextFileReader::detectAndHandleHeader()
+{
+ if (!isHeaderLine(_sLine)) {
+ return false;
+ }
+ if (!_fullHeaderFound) {
+ _header += _sLine;
+ _header += "\n"; //add new line, since it was chomped by getline
+ }
+ return true;
+}
+
+bool SingleLineDelimTextFileReader::findDelimiters() {
+ memset(_delimPositions, 0, (_numFields +1) * sizeof(int));
+ //scan the line for delimiters, determine their positions
+ _delimPositions[0] = -1;
+ int currField=1;
+ int len = (int)_sLine.size();
+ for (int i=0; i < len; i++) {
+ if (_sLine[i] == _delimChar) {
+ _delimPositions[currField] = i;
+ currField++;
+ }
+ }
+ _delimPositions[currField] = len;
+ if (currField != _numFields) {
+ cerr << "Error: line number " << _lineNum << " of file " << _filename << " has " << currField << " fields, but " << _numFields << " were expected." << endl;
+ exit(1);
+ }
+ return true;
+}
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
new file mode 100644
index 0000000..954ca2a
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
@@ -0,0 +1,46 @@
+/*
+ * SingleLineTextFileReader.h
+ *
+ * Created on: Nov 8, 2012
+ * Author: nek3d
+ */
+
+#ifndef SINGLELINETEXTFILEREADER_H_
+#define SINGLELINETEXTFILEREADER_H_
+
+using namespace std;
+
+#include "FileReader.h"
+#include "QuickString.h"
+
+class SingleLineDelimTextFileReader : public FileReader {
+public:
+ SingleLineDelimTextFileReader(int numFields, char delimChar = '\t');
+ ~SingleLineDelimTextFileReader();
+
+ virtual bool readEntry();
+ virtual int getNumFields() const { return _numFields; }
+ virtual void getField(int numField, QuickString &val) const;
+ virtual void getField(int numField, int &val); //this signaiture isn't const because it operates on an internal QuickString for speed.
+ virtual void getField(int fieldNum, char &val) const;
+ virtual void appendField(int fieldNum, QuickString &str) const;
+ virtual const QuickString &getHeader() const { return _header; }
+ virtual bool hasHeader() const { return _fullHeaderFound; }
+protected:
+ int _numFields;
+ char _delimChar;
+ QuickString _header;
+ bool _fullHeaderFound;
+ int _currDataPos;
+ QuickString _sLine;
+ int *_delimPositions;
+ QuickString _currChromStr;
+ QuickString _tempChrPosStr;
+ int _lineNum;
+ bool detectAndHandleHeader();
+ bool findDelimiters();
+
+};
+
+
+#endif /* SINGLELINETEXTFILEREADER_H_ */
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
new file mode 100644
index 0000000..dec5e31
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
@@ -0,0 +1,72 @@
+#include "SingleLineDelimTransferBuffer.h"
+#include <cstring>
+#include <iostream>
+#include <cstdio>
+#include <cstdlib>
+
+SingleLineDelimTransferBuffer::SingleLineDelimTransferBuffer(int numFields, char delimChar)
+: _numFields(numFields),
+ _delimChar(delimChar)
+{
+ _fields = new char *[_numFields];
+ for (int i=0; i < numFields; i++) {
+ _fields[i] = new char[MAX_FIELD_SIZE];
+ memset(_fields[i], 0, MAX_FIELD_SIZE);
+ }
+}
+
+SingleLineDelimTransferBuffer::~SingleLineDelimTransferBuffer()
+{
+ for (int i=0; i < _numFields; i++) {
+ delete [] _fields[i];
+ _fields[i] = NULL;
+ }
+ delete [] _fields;
+ _fields = NULL;
+}
+
+bool SingleLineDelimTransferBuffer::initFromInput(const char *inBuffer)
+{
+ clear();
+ if (strlen(inBuffer) == 0) {
+ return false;
+ }
+ const char *oldCursor = (const char *)inBuffer;
+ const char *newCursor = (const char *)inBuffer;
+ int fieldNum = 0;
+ while (oldCursor[0] != '\0' && oldCursor[0] != '\n') {
+ while (newCursor[0] != _delimChar && newCursor[0] != '\0') {
+ newCursor++;
+ }
+ if (newCursor != oldCursor) {
+ memcpy(_fields[fieldNum], oldCursor, newCursor - oldCursor);
+ fieldNum++;
+ }
+ if (newCursor[0] != '\0') {
+ oldCursor = newCursor +1;
+ newCursor = oldCursor;
+ } else {
+ break;
+ }
+ }
+ if (fieldNum == _numFields) {
+ return true;
+ }
+ return false;
+}
+
+const char *SingleLineDelimTransferBuffer::getField(int fieldNum) const
+{
+ if (fieldNum < _numFields) {
+ return _fields[fieldNum];
+ }
+ cerr << "Error: Requested field " << fieldNum << "from TransferBuffer with only " << _numFields << " fields." <<endl;
+ exit(1);
+}
+
+void SingleLineDelimTransferBuffer::clear(void)
+{
+ for (int i=0; i < _numFields; i++) {
+ memset(_fields[i], 0, MAX_FIELD_SIZE);
+ }
+}
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
new file mode 100644
index 0000000..9398ff7
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
@@ -0,0 +1,31 @@
+/*
+ * SingleLineDelimTransferBuffer.h
+ *
+ * Created on: Nov 8, 2012
+ * Author: nek3d
+ */
+
+#ifndef SINGLELINEDELIMTRANSFERBUFFER_H_
+#define SINGLELINEDELIMTRANSFERBUFFER_H_
+
+using namespace std;
+
+class SingleLineDelimTransferBuffer {
+public:
+ SingleLineDelimTransferBuffer(int numFields, char delim='\t');
+ ~SingleLineDelimTransferBuffer();
+ bool initFromInput(const char *inBuffer);
+ int getNumFields() const { return _numFields; }
+ const char *getField(int fieldNum) const;
+
+protected:
+ void clear();
+
+ static const int MAX_FIELD_SIZE = 8192; //Given field can not exceed 8K.
+ int _numFields;
+ char _delimChar;
+ char **_fields;
+};
+
+
+#endif /* SINGLELINEDELIMTRANSFERBUFFER_H_ */
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
new file mode 100644
index 0000000..38fc056
--- /dev/null
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -0,0 +1,398 @@
+
+#include "FileRecordMgr.h"
+#include "FreeList.h"
+#include "Record.h"
+#include "NewGenomeFile.h"
+
+FileRecordMgr::FileRecordMgr(const QuickString &filename, bool isSorted)
+:
+ _filename(filename),
+ _bufStreamMgr(NULL),
+ _fileReader(NULL),
+ _fileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
+ _recordType(FileRecordTypeChecker::UNKNOWN_RECORD_TYPE),
+ _recordMgr(NULL),
+ _isSortedInput(isSorted),
+ _freeListBlockSize(512),
+ _useFullBamTags(false),
+ _prevStart(INT_MAX),
+ _prevChromId(-1),
+ _mustBeForward(false),
+ _mustBeReverse(false),
+ _totalRecordLength(0),
+ _totalMergedRecordLength(0),
+ _blockMgr(NULL),
+ _bamReader(NULL),
+ _hasGenomeFile(false),
+ _genomeFile(NULL)
+{
+}
+
+FileRecordMgr::~FileRecordMgr(){
+
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+
+ close(); //just make sure file was closed.
+ delete _fileReader;
+ _fileReader = NULL;
+
+ delete _recordMgr;
+ _recordMgr = NULL;
+}
+
+bool FileRecordMgr::open(){
+ _bufStreamMgr = new BufferedStreamMgr(_filename);
+ if (!_bufStreamMgr->init()) {
+ cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+ exit(1);
+ }
+
+ _fileType = _bufStreamMgr->getTypeChecker().getFileType();
+ _recordType = _bufStreamMgr->getTypeChecker().getRecordType();
+ if (_fileType == FileRecordTypeChecker::UNKNOWN_FILE_TYPE || _recordType == FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
+ cerr << "Error: Unable to determine type for file " << _filename << endl;
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+ exit(1);
+ }
+ allocateFileReader();
+ _recordMgr = new RecordMgr(_recordType, _freeListBlockSize);
+
+ _fileReader->setFileName(_filename.c_str());
+ _fileReader->setInputStream(_bufStreamMgr);
+ if (!_fileReader->open()) {
+ cerr << "Error: Types determined but can't open file " << _filename << endl;
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+ exit(1);
+ }
+
+ return true;
+}
+
+void FileRecordMgr::close(){
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+
+ if (_fileReader != NULL) {
+ _fileReader->close();
+ delete _fileReader;
+ _fileReader = NULL;
+ }
+}
+
+bool FileRecordMgr::eof(){
+ return _fileReader->eof();
+}
+
+Record *FileRecordMgr::allocateAndGetNextRecord()
+{
+ if (!_fileReader->isOpen()) {
+ return NULL;
+ }
+ if (!_fileReader->readEntry()) {
+ return NULL;
+ }
+ Record *record = NULL;
+ record = _recordMgr->allocateRecord();
+ if (!record->initFromFile(_fileReader)) {
+ _recordMgr->deleteRecord(record);
+ return NULL;
+ }
+
+ // If the record is unmapped, don't test for valid coords or sort order,
+ // but still return it so the -v (noHit) option and the like will still
+ // see it.
+
+ if (!record->isUnmapped()) {
+ if (!record->coordsValid()) {
+ cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
+ exit(1);
+ }
+
+ //test for sorted order, if necessary.
+ if (_isSortedInput) {
+ testInputSortOrder(record);
+ }
+ }
+ assignChromId(record);
+ _totalRecordLength += (unsigned long)(record->getEndPos() - record->getStartPos());
+ return record;
+}
+
+void FileRecordMgr::assignChromId(Record *record) {
+ const QuickString &currChrom = record->getChrName();
+ if (currChrom != _prevChrom && _hasGenomeFile) {
+ _prevChromId = _genomeFile->getChromId(currChrom);
+ record->setChromId(_prevChromId);
+ } else {
+ record->setChromId(_prevChromId);
+ }
+}
+
+void FileRecordMgr::testInputSortOrder(Record *record)
+{
+ // User specified that file must be sorted. Check that it is so.
+ // TBD: In future versions, we might not want/need all files to be sorted,
+ // even if the -sorted option is used, depending on number of input files
+ // and program being run. Should that occur, this block will need adjusting.
+ // NEK - 9/5/13
+
+
+ // Special: For BAM records that aren't mapped, we actually don't want
+ // to test the sort order. Another ugly hack sponsored by the letters B, A, and M.
+ if (record->isUnmapped()) {
+ return;
+ }
+
+
+ const QuickString &currChrom = record->getChrName();
+ int currStart = record->getStartPos();
+ if (record->isZeroLength()) {
+ currStart++;
+ }
+ if (currChrom != _prevChrom) {
+ if ( _foundChroms.find(currChrom) != _foundChroms.end()) {
+ //this is a different chrom than the last record had, but we've already seen this chrom.
+ sortError(record, false);
+ } else {
+ //new chrom has not been seen before.
+ //TBD: test genome file for ChromId.
+ if (_hasGenomeFile) {
+ int currChromId = _genomeFile->getChromId(currChrom);
+ if (currChromId < _prevChromId) {
+ sortError(record, true);
+ } else {
+ _prevChromId = currChromId;
+ }
+ }
+ _foundChroms.insert(currChrom);
+ _prevChrom = currChrom;
+ _prevStart = INT_MAX;
+ record->setChromId(_prevChromId);
+ }
+ } else if (currStart < _prevStart) { //same chrom as last record, but with lower startPos, so still out of order.
+ sortError(record, false);
+ }
+ _prevStart = currStart;
+
+}
+
+void FileRecordMgr::sortError(const Record *record, bool genomeFileError)
+{
+ if (genomeFileError) {
+ cerr << "Error: Sorted input specified, but the file " << _filename << " has the following record with a different sort order than the genomeFile " <<
+ _genomeFile->getGenomeFileName() << endl;
+ } else {
+ cerr << "Error: Sorted input specified, but the file " << _filename << " has the following out of order record" << endl;
+ }
+ cerr << *record << endl;
+ exit(1);
+}
+
+
+void FileRecordMgr::deleteRecord(const Record *record) {
+ _recordMgr->deleteRecord(record);
+}
+
+void FileRecordMgr::allocateFileReader()
+{
+ switch (_fileType) {
+ case FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE:
+ case FileRecordTypeChecker::VCF_FILE_TYPE:
+ _fileReader = new SingleLineDelimTextFileReader(_bufStreamMgr->getTypeChecker().getNumFields(), _bufStreamMgr->getTypeChecker().getDelimChar());
+ break;
+
+ case FileRecordTypeChecker::BAM_FILE_TYPE:
+ _fileReader = new BamFileReader();
+ (static_cast<BamFileReader *>(_fileReader))->setUseTags(_useFullBamTags);
+ (static_cast<BamFileReader *>(_fileReader))->setBamReader(_bufStreamMgr->getBamReader());
+ break;
+ default:
+ break;
+ }
+}
+
+const BamTools::RefVector & FileRecordMgr::getBamReferences() {
+ // exta safety check to insure user checked the file type first.
+ if (_fileType != FileRecordTypeChecker::BAM_FILE_TYPE) {
+ cerr << "Error: Attempted to get BAM references from file " << _filename << ", which is NOT a BAM file." << endl;
+ exit(1);
+ }
+ return static_cast<BamFileReader *>(_fileReader)->getReferences();
+}
+
+#ifdef false
+
+Record *FileRecordMgr::allocateAndGetNextMergedRecord(WANT_STRAND_TYPE desiredStrand, int maxDistance) {
+ RecordKeyList recList;
+ if (!allocateAndGetNextMergedRecord(recList, desiredStrand, maxDistance)) {
+ return NULL;
+ }
+ deleteAllMergedItemsButKey(recList);
+ return const_cast<Record *>(recList.getKey()); //want key to be non-const
+}
+
+bool FileRecordMgr::allocateAndGetNextMergedRecord(RecordKeyList & recList, WANT_STRAND_TYPE desiredStrand, int maxDistance)
+{
+ if (!recList.allClear()) {
+ deleteMergedRecord(recList);
+ }
+
+ _mustBeForward = desiredStrand == SAME_STRAND_FORWARD;
+ _mustBeReverse = desiredStrand == SAME_STRAND_REVERSE;
+
+ Record *startRecord = tryToTakeFromStorage();
+
+ // if we couldn't use a previously stored record for starters,
+ //then begin with a new one that matches strand criteria.
+ while (startRecord == NULL) {
+ startRecord = allocateAndGetNextRecord();
+ if (startRecord == NULL) { //hit EOF!!
+ return false;
+ }
+
+ if (_mustBeForward && !startRecord->getStrand()) {
+ //record is reverse, wanted forward.
+ addToStorage(startRecord);
+ startRecord = NULL;
+ } else if (_mustBeReverse && startRecord->getStrand()) {
+ //record is forward, wanted reverse
+ addToStorage(startRecord);
+ startRecord = NULL;
+ }
+ }
+
+ // OK!! We have a start record!
+
+ _mustBeForward = desiredStrand == SAME_STRAND_FORWARD || (desiredStrand == SAME_STRAND_EITHER && startRecord->getStrand());
+ _mustBeReverse = desiredStrand == SAME_STRAND_REVERSE || (desiredStrand == SAME_STRAND_EITHER && !startRecord->getStrand());
+
+ const QuickString &currChrom = startRecord->getChrName();
+ _foundChroms.insert(currChrom);
+
+ bool madeComposite = false;
+ recList.push_back(startRecord);
+ recList.setKey(startRecord); //key of recList will just be the startRecord unless we're able to merge more.
+
+ bool currStrand = startRecord->getStrand();
+ bool mustMatchStrand = desiredStrand != ANY_STRAND;
+
+ int currEnd = startRecord->getEndPos();
+ //now look for more records to merge with this one.
+ //stop when they're out of range, not on the same chromosome, or we hit EOF.
+ //ignore if they don't comply with strand.
+ Record *nextRecord = NULL;
+ while (nextRecord == NULL) {
+ bool takenFromStorage = false;
+ nextRecord = mustMatchStrand ? tryToTakeFromStorage(currStrand) : tryToTakeFromStorage();
+ if (nextRecord == NULL) {
+ nextRecord = allocateAndGetNextRecord();
+ } else {
+ takenFromStorage = true;
+ }
+ if (nextRecord == NULL) { // EOF hit
+ break;
+ }
+ const QuickString &newChrom = nextRecord->getChrName();
+ if (newChrom != currChrom) { //hit a different chromosome.
+ if (_foundChroms.find(newChrom) == _foundChroms.end() || takenFromStorage) {
+ //haven't seen this chromosome before.
+ addToStorage(nextRecord);
+ break;
+ } else {
+ //different strand, but we've already seen this chrom. File is not sorted.
+ fprintf(stderr, "ERROR: Input file %s is not sorted by chromosome, startPos.\n", _context->getInputFileName(_contextFileIdx).c_str());
+ deleteRecord(nextRecord);
+ deleteMergedRecord(recList);
+ exit(1);
+ }
+ }
+ int nextStart = nextRecord->getStartPos();
+ //is the record out of range?
+ if (nextStart > currEnd + maxDistance) {
+ //yes, it's out of range.
+ addToStorage(nextRecord);
+ break;
+ }
+
+ //ok, they're on the same chrom and in range. Are we happy with the strand?
+ if (mustMatchStrand && nextRecord->getStrand() != currStrand) {
+ //no, we're not.
+ addToStorage(nextRecord);
+ nextRecord = NULL;
+ continue;
+ }
+ //everything's good! do a merge.
+ recList.push_back(nextRecord);
+ madeComposite = true;
+ int nextEnd = nextRecord->getEndPos();
+ if (nextEnd > currEnd) {
+ currEnd = nextEnd;
+ }
+ nextRecord = NULL;
+ }
+ if (madeComposite) {
+ Record *newKey = _recordMgr->allocateRecord();
+ (*newKey) = (*startRecord);
+ newKey->setEndPos(currEnd);
+ recList.setKey(newKey);
+ }
+ _totalMergedRecordLength += (unsigned long)(recList.getKey()->getEndPos() - recList.getKey()->getStartPos());
+ return true;
+}
+
+void FileRecordMgr::addToStorage(Record *record) {
+ _storedRecords.push(record);
+}
+
+Record *FileRecordMgr::tryToTakeFromStorage() {
+ Record *record = _storedRecords.empty() ? NULL : const_cast<Record *>(_storedRecords.top());
+ if (record != NULL) {
+ _storedRecords.pop();
+ }
+ return record;
+}
+
+Record *FileRecordMgr::tryToTakeFromStorage(bool strand) {
+ Record *record = NULL;
+ if(strand) {
+ if (_storedRecords.emptyForward()) {
+ return NULL;
+ } else {
+ record = const_cast<Record *>(_storedRecords.topForward());
+ _storedRecords.popForward();
+ return record;
+ }
+ } else {
+ if (_storedRecords.emptyReverse()) {
+ return NULL;
+ } else {
+ record = const_cast<Record *>(_storedRecords.topReverse());
+ _storedRecords.popReverse();
+ return record;
+ }
+ }
+}
+
+void FileRecordMgr::deleteMergedRecord(RecordKeyList &recList)
+{
+ deleteAllMergedItemsButKey(recList);
+ deleteRecord(recList.getKey());
+ recList.setKey(NULL);
+}
+
+void FileRecordMgr::deleteAllMergedItemsButKey(RecordKeyList &recList) {
+ //if the key is also in the list, this method won't delete it.
+ for (RecordKeyList::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
+ if (iter->value() == recList.getKey()) {
+ continue;
+ }
+ deleteRecord(iter->value());
+ }
+ recList.clearList();
+}
+#endif
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
new file mode 100644
index 0000000..b4e76e9
--- /dev/null
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -0,0 +1,193 @@
+/*
+ * FileRecordMgr.h
+ *
+ * Created on: Nov 8, 2012
+ * Author: nek3d
+ */
+
+#ifndef FILERECORDMGR_H_
+#define FILERECORDMGR_H_
+
+using namespace std;
+
+#include <string>
+#include "QuickString.h"
+#include <set>
+//#include "DualQueue.h"
+
+//include headers for all FileReader and derivative classes.
+#include "BufferedStreamMgr.h"
+#include "FileReader.h"
+#include "SingleLineDelimTextFileReader.h"
+#include "BamFileReader.h"
+
+//record manager and all record classes
+#include "RecordMgr.h"
+
+#include "RecordKeyList.h"
+#include "BlockMgr.h"
+
+class Record;
+class NewGenomeFile;
+
+class FileRecordMgr {
+public:
+ FileRecordMgr(const QuickString & filename, bool isSorted = false);
+ ~FileRecordMgr();
+ bool open();
+ void close();
+ bool eof();
+
+ const QuickString &getFileName() const { return _filename;}
+ bool hasHeader() const { return _fileReader->hasHeader(); }
+ const QuickString &getHeader() const { return _fileReader->getHeader(); }
+
+ bool recordsHaveName() const {
+ return _bufStreamMgr->getTypeChecker().recordTypeHasName(_recordType);
+ }
+ bool recordsHaveScore() const {
+ return _bufStreamMgr->getTypeChecker().recordTypeHasScore(_recordType);
+ }
+ bool recordsHaveStrand() const {
+ return _bufStreamMgr->getTypeChecker().recordTypeHasStrand(_recordType);
+ }
+
+ FileRecordTypeChecker::FILE_TYPE getFileType() const {
+ return _fileType;
+ }
+ FileRecordTypeChecker::RECORD_TYPE getRecordType() const {
+ return _recordType;
+ }
+ const string &getFileTypeName() const {
+ return _bufStreamMgr->getTypeChecker().getFileTypeName();
+ }
+
+ const string &getRecordTypeName() const {
+ return _bufStreamMgr->getTypeChecker().getRecordTypeName();
+ }
+
+ const BamTools::RefVector &getBamReferences();
+
+ int getNumFields() const { return _fileReader->getNumFields(); }
+ //This is an all-in-one method to give the user a new record that is initialized with
+ //the next entry in the data file.
+ //NOTE!! User MUST pass back the returned pointer to deleteRecord method for cleanup!
+ //Also Note! User must check for NULL returned, meaning we failed to get the next record.
+ Record *allocateAndGetNextRecord();
+ void deleteRecord(const Record *);
+
+#ifdef false
+ //////////////////////////////////////////////////////////////////////////////////
+ //
+ // MERGED RECORDS
+ //
+ //this will give a single "meta" record containing "flattened" or merged records.
+ //
+ // 1st ARG: Pass an empty RecordKeyList. When done, will have a pair: 1st is the final merged record,
+ // second is list of constituent Records merged.
+ // ** NOTE ** If the RecordKeyList is not empty, this method will empty it for you and delete all contents!
+ //
+ // 2nd ARG: Choose from WANT_STRAND_TYPE, defined below below
+ //
+ // 3rd ARG: allows for nearby records, i.e. maxDistance 100 will merge records <= 100 bases apart. Default 0 means only
+ // merge records that actually intersect.
+ //
+ // Return value: true if any records found. False if eof hit before records matching requested parameters found.
+
+ typedef enum { SAME_STRAND_FORWARD, //must all be forward strand
+ SAME_STRAND_REVERSE, //must all be reverse strand
+ SAME_STRAND_EITHER, //must be same strand, but can be either forward or reverse
+ ANY_STRAND } //do no care about strand (Default value)
+ WANT_STRAND_TYPE;
+
+ //
+ // WARNING!! Specifying a strand will keep all records on the other strand in memory!!
+ // This is done so that requests for records on that other strand can still be met.
+ // For now, use this method at any time to purge the kept records from memory, such as
+ // when changing chromosomes, for example.
+ void purgeKeepList();
+ bool allocateAndGetNextMergedRecord(RecordKeyList & recList, WANT_STRAND_TYPE desiredStrand = ANY_STRAND, int maxDistance = 0);
+ void deleteMergedRecord(RecordKeyList &recList); // MUST use this method for cleanup!
+
+ //this method will allocate a new record of merged records, but the returned record should only be passed to the deleteRecord method
+ //for cleanup, not to the delete mmerged record.
+ Record *allocateAndGetNextMergedRecord(WANT_STRAND_TYPE desiredStrand = ANY_STRAND, int maxDistance = 0);
+
+ //
+ // END MERGED RECORDS
+ //
+ //////////////////////////////////////////////////////////////////////////////////
+#endif
+
+ //File statistics
+ unsigned long getTotalRecordLength() const { return _totalRecordLength; } //sum of length of all returned records
+ unsigned long getTotalMergedRecordLength() const { return _totalMergedRecordLength; } // sum of all merged intervals
+
+
+
+ //Setting the freeListBlockSize is optional. If the user never calls this,
+ //the blockSize defaults to 512.
+ void setFreeListBlockSize(int blockSize) { _freeListBlockSize = blockSize; }
+
+ //special: For BAM files, our default is to not use all the
+ //tag information in a BAM file, which reduces the run time in some
+ //cases by more than 50%. But setting this method to true
+ //will use all the tags, if more information is desired.
+ //MUST BE CALLED BEFORE THE BAM FILE IS OPEN.
+ void setFullBamFlags(bool flag) { _useFullBamTags = flag; }
+ void setGenomeFile(NewGenomeFile *genomeFile) {
+ _genomeFile = genomeFile;
+ _hasGenomeFile = true;
+ }
+
+private:
+ QuickString _filename;
+ BufferedStreamMgr *_bufStreamMgr;
+
+ FileReader *_fileReader;
+ FileRecordTypeChecker::FILE_TYPE _fileType;
+ FileRecordTypeChecker::RECORD_TYPE _recordType;
+ RecordMgr *_recordMgr;
+ bool _isSortedInput;
+ int _freeListBlockSize;
+ bool _useFullBamTags;
+
+ //members for enforcing sorted order.
+ set<QuickString> _foundChroms;
+ QuickString _prevChrom;
+ int _prevStart;
+ int _prevChromId;
+
+ //members for handling merged records
+// DualQueue<Record *, DualQueueAscending > _storedRecords;
+
+ bool _mustBeForward;
+ bool _mustBeReverse;
+
+ //available stats after run
+ unsigned long _totalRecordLength;
+ unsigned long _totalMergedRecordLength;
+
+ BlockMgr *_blockMgr;
+ BamTools::BamReader *_bamReader;
+ bool _hasGenomeFile;
+ NewGenomeFile *_genomeFile;
+
+ void allocateFileReader();
+ void testInputSortOrder(Record *record);
+ void assignChromId(Record *);
+ void sortError(const Record *record, bool genomeFileError);
+
+
+#ifdef false
+ void deleteAllMergedItemsButKey(RecordKeyList &recList);
+ void addToStorage(Record *record);
+ Record *tryToTakeFromStorage();
+ Record *tryToTakeFromStorage(bool strand);
+#endif
+
+
+};
+
+
+#endif /* FILERECORDMGR_H_ */
diff --git a/src/utils/FileRecordTools/Makefile b/src/utils/FileRecordTools/Makefile
new file mode 100644
index 0000000..9d02117
--- /dev/null
+++ b/src/utils/FileRecordTools/Makefile
@@ -0,0 +1,51 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+SUBDIRS = ./FileReaders \
+ ./Records \
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= FileRecordMgr.cpp FileRecordMgr.h
+OBJECTS= FileRecordMgr.o RecordOutputMgr.o
+_EXT_OBJECTS=SingleLineDelimTextFileReader.o BamFileReader.o Bed3Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
+ SingleLineDelimTransferBuffer.o FileRecordTypeChecker.o QuickString.o ParseTools.o RecordKeyList.o BufferedStreamMgr.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
+ @echo " * compiling FileRecordMgr.cpp"
+ @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+
+
+.PHONY: $(SUBDIRS)
+$(SUBDIRS): $(OBJ_DIR)
+ @echo "- Building in $@"
+ @$(MAKE) --no-print-directory --directory=$@
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/FileRecordMgr.o
+ @rm -f $(OBJ_DIR)/RecordMgr.o
+ @rm -f $(OBJ_DIR)/FileRecordTypeChecker.o
+ @rm -f $(OBJ_DIR)/SingleLineDelimTextFileReader.o
+ @rm -f $(OBJ_DIR)/SingleLineDelimTransferBuffer.o
+
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
new file mode 100644
index 0000000..4c5cd8d
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -0,0 +1,176 @@
+/*
+ * BamRecord.cpp
+ *
+ * Created on: Jan 14, 2014
+ * Author: nek3d
+ */
+
+#include "BamRecord.h"
+#include "BamFileReader.h"
+#include "RecordKeyList.h"
+
+BamRecord::BamRecord()
+: _bamChromId(-1)
+{
+
+}
+
+BamRecord::~BamRecord()
+{
+
+}
+
+const BamRecord &BamRecord::operator=(const BamRecord &other)
+{
+ Bed6Interval::operator=(other);
+ _bamAlignment = other._bamAlignment;
+ return *this;
+}
+
+
+bool BamRecord::initFromFile(FileReader *fileReader)
+{
+ BamFileReader *bamFileReader = static_cast<BamFileReader*>(fileReader);
+ return initFromFile(bamFileReader);
+
+}
+
+bool BamRecord::initFromFile(BamFileReader *bamFileReader)
+{
+ bamFileReader->getChrName(_chrName);
+
+ _bamChromId = bamFileReader->getCurrChromdId();
+ _startPos = bamFileReader->getStartPos();
+ int2str(_startPos, _startPosStr);
+ _endPos = bamFileReader->getEndPos();
+ int2str(_endPos, _endPosStr);
+ bamFileReader->getName(_name);
+ bamFileReader->getScore(_score);
+ char strandChar = bamFileReader->getStrand();
+ setStrand(strandChar);
+
+ _bamAlignment = bamFileReader->getAlignment();
+ _isUnmapped = !_bamAlignment.IsMapped();
+ _isMateUnmapped = !_bamAlignment.IsMateMapped();
+ return true;
+}
+
+void BamRecord::clear()
+{
+ Bed6Interval::clear();
+ _bamChromId = -1;
+
+
+ //Clear the BamAlignment object. Sadly, it does not have a clear() method,
+ //so we have to do each member manually.
+ _bamAlignment.Name.clear();
+ _bamAlignment.Length = 0;
+ _bamAlignment.QueryBases.clear();
+ _bamAlignment.AlignedBases.clear();
+ _bamAlignment.Qualities.clear();
+ _bamAlignment.TagData.clear();
+ _bamAlignment.RefID = -1;
+ _bamAlignment.Position = -1;
+ _bamAlignment.Bin = 0;
+ _bamAlignment.MapQuality = 0;
+ _bamAlignment.AlignmentFlag = 0;
+ _bamAlignment.CigarData.clear();
+ _bamAlignment.MateRefID = -1;
+ _bamAlignment.MatePosition = -1;
+ _bamAlignment.InsertSize = -1;
+ _bamAlignment.Filename.clear();
+
+ _bamAlignment.SupportData.AllCharData.clear();
+ _bamAlignment.SupportData.BlockLength = 0;
+ _bamAlignment.SupportData.NumCigarOperations = 0;
+ _bamAlignment.SupportData.QueryNameLength = 0;
+ _bamAlignment.SupportData.QuerySequenceLength = 0;
+ _bamAlignment.SupportData.HasCoreOnly = false;
+
+ _bamAlignment.ErrorString.clear();
+
+
+}
+
+void BamRecord::print(QuickString &outBuf, RecordKeyList *keyList) const
+{
+ Bed6Interval::print(outBuf);
+ printRemainingBamFields(outBuf, keyList);
+}
+
+void BamRecord::print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const
+{
+ Bed6Interval::print(outBuf, start, end);
+ printRemainingBamFields(outBuf, keyList);
+}
+
+void BamRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const
+{
+ Bed6Interval::print(outBuf, start, end);
+ printRemainingBamFields(outBuf, keyList);
+}
+
+void BamRecord::printNull(QuickString &outBuf) const
+{
+ Bed6Interval::printNull(outBuf);
+ outBuf.append("\t.\t.\t.\t.\t.\t.", 12);
+}
+
+void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const
+{
+ outBuf.append('\t');
+ outBuf.append(_bamAlignment.Position);
+ outBuf.append('\t');
+ outBuf.append(_endPos);
+ outBuf.append("\t0,0,0", 6);
+ outBuf.append('\t');
+
+ int numBlocks = (int)keyList->size();
+
+ if (numBlocks > 0) {
+ outBuf.append(numBlocks);
+
+ vector<int> blockLengths;
+ vector<int> blockStarts;
+ for (RecordKeyList::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
+ const Record *block = iter->value();
+ blockLengths.push_back(block->getEndPos() - block->getStartPos());
+ blockStarts.push_back(block->getStartPos() - _bamAlignment.Position);
+ }
+
+ outBuf.append('\t');
+ for (int i=0; i < (int)blockLengths.size(); i++) {
+ outBuf.append(blockLengths[i]);
+ outBuf.append(',');
+ }
+ outBuf.append('\t');
+ for (int i=0; i < (int)blockStarts.size(); i++) {
+ outBuf.append( blockStarts[i]);
+ outBuf.append(',');
+ }
+ }
+ else {
+ outBuf.append("1\t0,\t0,");
+ }
+}
+
+void BamRecord::printUnmapped(QuickString &outBuf) const {
+ outBuf.append(_chrName.empty() ? "." : _chrName);
+ outBuf.append("\t-1\t-1\t");
+ outBuf.append(_name.empty() ? "." : _name);
+ outBuf.append('\t');
+ outBuf.append(_score.empty() ? "." : _score);
+ outBuf.append("\t.\t-1\t-1\t-1\t0,0,0\t0\t.\t."); // dot for strand, -1 for blockStarts and blockEnd
+}
+
+const QuickString &BamRecord::getField(int fieldNum) const
+{
+ //TBD: Determine what correct behavior should be.
+ //I.e. if users requests field 2, do they want Flag
+ //for Bam Records, or startPos for all records? -NEK 1/14/14.
+
+ return Bed6Interval::getField(fieldNum);
+}
+
+
+
diff --git a/src/utils/FileRecordTools/Records/BamRecord.h b/src/utils/FileRecordTools/Records/BamRecord.h
new file mode 100644
index 0000000..b74dbc2
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BamRecord.h
@@ -0,0 +1,55 @@
+/*
+ * BamRecord.h
+ *
+ * Created on: Dec 4, 2012
+ * Author: nek3d
+ */
+
+#ifndef BAMRECORD_H_
+#define BAMRECORD_H_
+
+#include "Bed6Interval.h"
+#include "ParseTools.h"
+#include "QuickString.h"
+#include "api/BamAlignment.h"
+
+class FileReader;
+class BamFileReader;
+class RecordKeyList;
+
+class BamRecord : public Bed6Interval {
+public:
+ friend class FreeList<BamRecord>;
+
+ BamRecord();
+ virtual const BamRecord &operator=(const BamRecord &);
+ bool initFromFile(FileReader *);
+ virtual bool initFromFile(BamFileReader *);
+ virtual void clear();
+ virtual void print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const;
+ virtual void print(QuickString &outBuf, RecordKeyList *keyList) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual void printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const;
+ virtual void printUnmapped(QuickString &outBuf) const;
+
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BAM_RECORD_TYPE; }
+
+ const BamTools::BamAlignment &getAlignment() const { return _bamAlignment; }
+ int getBamChromId() const { return _bamChromId; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 12; }
+
+protected:
+ BamTools::BamAlignment _bamAlignment;
+ int _bamChromId; //different from chromId, because BAM file may be in different order
+ //than the genomeFile.
+
+ virtual ~BamRecord();
+ void printRemainingBamFields();
+
+};
+
+
+#endif /* BAMRECORD_H_ */
diff --git a/src/utils/FileRecordTools/Records/Bed12Interval.cpp b/src/utils/FileRecordTools/Records/Bed12Interval.cpp
new file mode 100644
index 0000000..867a69e
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed12Interval.cpp
@@ -0,0 +1,148 @@
+#include "Bed12Interval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstdlib>
+
+Bed12Interval::Bed12Interval()
+:_thickStart(-1),
+ _thickEnd(-1),
+ _blockCount(-1)
+
+{
+}
+
+Bed12Interval::~Bed12Interval()
+{
+}
+const Bed12Interval &Bed12Interval::operator=(const Bed12Interval &other) {
+ Bed6Interval::operator=(other);
+
+ _thickStart = other._thickStart;
+ _thickEnd = other._thickEnd;
+ _itemRGB = other._itemRGB;
+ _blockCount = other._blockCount;
+ _blockSizes = other._blockSizes;
+ _blockStarts = other._blockStarts;
+
+ return *this;
+}
+
+bool Bed12Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ bool baseRetFlag = Bed6Interval::initFromFile(fileReader);
+
+ fileReader->getField(6, _thickStartStr);
+ fileReader->getField(7, _thickEndStr);
+ fileReader->getField(8, _itemRGB);
+ fileReader->getField(9, _blockCountStr);
+ fileReader->getField(10, _blockSizes);
+ fileReader->getField(11, _blockStarts);
+
+ _thickStart = str2chrPos(_thickStartStr);
+ _thickEnd = str2chrPos(_thickEndStr);
+ _blockCount = str2chrPos(_blockCountStr);
+ return baseRetFlag;
+}
+
+void Bed12Interval::clear() {
+ Bed6Interval::clear();
+
+ _thickStart = -1;
+ _thickEnd = -1;
+ _itemRGB.clear();
+ _blockCount = -1;
+ _blockSizes.clear();
+ _blockStarts.clear();
+ _thickStartStr.clear();
+ _thickEndStr.clear();
+ _blockCountStr.clear();
+
+}
+
+void Bed12Interval::print(QuickString &outBuf) const
+{
+ Bed6Interval::print(outBuf);
+
+ outBuf.append('\t');
+ outBuf.append(_thickStartStr);
+ outBuf.append('\t');
+ outBuf.append(_thickEndStr);
+ outBuf.append('\t');
+ outBuf.append(_itemRGB);
+ outBuf.append('\t');
+ outBuf.append(_blockCountStr);
+ outBuf.append('\t');
+ outBuf.append(_blockSizes);
+ outBuf.append('\t');
+ outBuf.append(_blockStarts);
+}
+
+void Bed12Interval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed6Interval::print(outBuf, start, end);
+
+ outBuf.append('\t');
+ outBuf.append(_thickStartStr);
+ outBuf.append('\t');
+ outBuf.append(_thickEndStr);
+ outBuf.append('\t');
+ outBuf.append(_itemRGB);
+ outBuf.append('\t');
+ outBuf.append(_blockCountStr);
+ outBuf.append('\t');
+ outBuf.append(_blockSizes);
+ outBuf.append('\t');
+ outBuf.append(_blockStarts);
+}
+
+void Bed12Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed6Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_thickStartStr);
+ outBuf.append('\t');
+ outBuf.append(_thickEndStr);
+ outBuf.append('\t');
+ outBuf.append(_itemRGB);
+ outBuf.append('\t');
+ outBuf.append(_blockCountStr);
+ outBuf.append('\t');
+ outBuf.append(_blockSizes);
+ outBuf.append('\t');
+ outBuf.append(_blockStarts);
+}
+
+
+void Bed12Interval::printNull(QuickString &outBuf) const
+{
+ Bed6Interval::printNull(outBuf);
+
+ outBuf.append("\t.\t.\t.\t.\t.\t.", 12);
+}
+
+const QuickString &Bed12Interval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 7:
+ return _thickStartStr;
+ break;
+ case 8:
+ return _thickEndStr;
+ break;
+ case 9:
+ return _itemRGB;
+ break;
+ case 10:
+ return _blockCountStr;
+ break;
+ case 11:
+ return _blockSizes;
+ break;
+ case 12:
+ return _blockStarts;
+ break;
+ default:
+ return Bed6Interval::getField(fieldNum);
+ break;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/Bed12Interval.h b/src/utils/FileRecordTools/Records/Bed12Interval.h
new file mode 100644
index 0000000..711800c
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed12Interval.h
@@ -0,0 +1,77 @@
+/*
+ * Bed12Interval.h
+ *
+ * Created on: Nov 28, 2012
+ * Author: nek3d
+ */
+
+#ifndef BED12INTERVAL_H_
+#define BED12INTERVAL_H_
+
+#include "Bed6Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+
+class Bed12Interval : public Bed6Interval {
+public:
+ friend class FreeList<Bed12Interval>;
+
+ Bed12Interval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void clear();
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED12_RECORD_TYPE; }
+
+ const Bed12Interval &operator=(const Bed12Interval &other);
+
+ virtual int getThickStart() const { return _thickStart; }
+ virtual void setThickStart(int thickStart) { _thickStart = thickStart; }
+
+ virtual int getThickEnd() const { return _thickEnd; }
+ virtual void setThickEnd(int thickEnd) { _thickEnd = thickEnd; }
+
+ virtual const QuickString & getItemRGB() const { return _itemRGB; }
+ virtual void setItemRGB(const QuickString & rgb) { _itemRGB = rgb; }
+ virtual void setItemRGB(const string & rgb) { _itemRGB = rgb; }
+ virtual void setItemRGB(const char *rgb) { _itemRGB = rgb; }
+
+ virtual int getBlockCount() const { return _blockCount; }
+ virtual void setBlockCount(int blockCount) { _blockCount = blockCount; }
+
+ virtual const QuickString & getBlockSizes() const { return _blockSizes; }
+ virtual void setBlockSizes(const QuickString & blockSizes) { _blockSizes = blockSizes; }
+ virtual void setBlockSizes(const string & blockSizes) { _blockSizes = blockSizes; }
+ virtual void setBlockSizes(const char *blockSizes) { _blockSizes = blockSizes; }
+
+ virtual const QuickString & getBlockStarts() const { return _blockStarts; }
+ virtual void setBlockStarts(const QuickString & blockStarts) { _blockStarts = blockStarts; }
+ virtual void setBlockStarts(const string & blockStarts) { _blockStarts = blockStarts; }
+ virtual void setBlockStarts(const char *blockStarts) { _blockStarts = blockStarts; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 12; }
+
+
+protected:
+ virtual ~Bed12Interval();
+
+ int _thickStart;
+ int _thickEnd;
+ QuickString _itemRGB;
+ int _blockCount;
+ QuickString _blockSizes;
+ QuickString _blockStarts;
+
+ //store int values as their originial strings for faster outputting.
+ QuickString _thickStartStr;
+ QuickString _thickEndStr;
+ QuickString _blockCountStr;
+};
+
+
+
+#endif /* BED12INTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.cpp b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
new file mode 100644
index 0000000..3f896be
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
@@ -0,0 +1,81 @@
+
+#include "Bed3Interval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstdio>
+#include <cstdlib>
+
+Bed3Interval::Bed3Interval()
+{
+
+}
+
+Bed3Interval::~Bed3Interval()
+{
+
+}
+
+bool Bed3Interval::initFromFile(FileReader *fileReader)
+{
+ SingleLineDelimTextFileReader *sldFileReader = static_cast<SingleLineDelimTextFileReader*>(fileReader);
+ return initFromFile(sldFileReader);
+}
+
+
+bool Bed3Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ fileReader->getField(0, _chrName);
+ fileReader->getField(1, _startPosStr);
+ fileReader->getField(2, _endPosStr);
+ _startPos = str2chrPos(_startPosStr);
+ _endPos = str2chrPos(_endPosStr);
+ return true;
+}
+
+void Bed3Interval::print(QuickString &outBuf) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_startPos);
+ outBuf.append('\t');
+ outBuf.append(_endPos);
+}
+
+void Bed3Interval::print(QuickString &outBuf, int start, int end) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(start);
+ outBuf.append('\t');
+ outBuf.append(end);
+}
+
+void Bed3Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(start);
+ outBuf.append('\t');
+ outBuf.append(end);
+}
+
+void Bed3Interval::printNull(QuickString &outBuf) const {
+ outBuf.append(".\t-1\t-1", 7);
+}
+
+const QuickString &Bed3Interval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 1:
+ return _chrName;
+ break;
+ case 2:
+ return _startPosStr;
+ break;
+ case 3:
+ return _endPosStr;
+ break;
+ default:
+ return Record::getField(fieldNum);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.h b/src/utils/FileRecordTools/Records/Bed3Interval.h
new file mode 100644
index 0000000..9f1ff11
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed3Interval.h
@@ -0,0 +1,43 @@
+/*
+ * Bed3Interval.h
+ *
+ * Created on: Nov 8, 2012
+ * Author: nek3d
+ */
+
+#ifndef BED3INTERVAL_H_
+#define BED3INTERVAL_H_
+
+#include "Record.h"
+#include "ParseTools.h"
+#include "QuickString.h"
+
+class FileReader;
+class SingleLineDelimTextFileReader;
+
+
+class Bed3Interval : public Record {
+public:
+ friend class FreeList<Bed3Interval>;
+
+ Bed3Interval();
+ bool initFromFile(FileReader *);
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED3_RECORD_TYPE; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 3; }
+
+protected:
+ virtual ~Bed3Interval();
+
+ bool _skipFirstThreeFieldsWhenPrinting;
+
+};
+
+
+#endif /* BED3INTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.cpp b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
new file mode 100644
index 0000000..c1ef81a
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
@@ -0,0 +1,62 @@
+#include "Bed4Interval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstring>
+
+Bed4Interval::Bed4Interval()
+{
+
+}
+
+Bed4Interval::~Bed4Interval()
+{
+
+}
+
+bool Bed4Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ bool baseRetFlag = Bed3Interval::initFromFile(fileReader);
+
+ fileReader->getField(3, _name);
+ return baseRetFlag;
+}
+
+void Bed4Interval::print(QuickString &outBuf) const
+{
+ Bed3Interval::print(outBuf);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+void Bed4Interval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+void Bed4Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+void Bed4Interval::printNull(QuickString &outBuf) const
+{
+ Bed3Interval::printNull(outBuf);
+ outBuf.append('\t');
+ outBuf.append("\t.", 2);
+}
+
+const QuickString &Bed4Interval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 4:
+ return _name;
+ break;
+ default:
+ return Bed3Interval::getField(fieldNum);
+ break;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.h b/src/utils/FileRecordTools/Records/Bed4Interval.h
new file mode 100644
index 0000000..f42817c
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed4Interval.h
@@ -0,0 +1,38 @@
+/*
+ * Bed4Interval.h
+ *
+ * Created on: Jun 27, 2013
+ * Author: nek3d
+ */
+
+#ifndef BED4INTERVAL_H_
+#define BED4INTERVAL_H_
+
+
+
+#include "Bed3Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+class Bed4Interval : public Bed3Interval {
+public:
+ friend class FreeList<Bed4Interval>;
+
+ Bed4Interval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED4_RECORD_TYPE; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 4; }
+
+
+protected:
+ virtual ~Bed4Interval();
+};
+
+
+#endif /* BED4INTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.cpp b/src/utils/FileRecordTools/Records/Bed5Interval.cpp
new file mode 100644
index 0000000..7307fb6
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed5Interval.cpp
@@ -0,0 +1,72 @@
+#include "Bed5Interval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstring>
+
+Bed5Interval::Bed5Interval()
+{
+
+}
+
+Bed5Interval::~Bed5Interval()
+{
+
+}
+
+bool Bed5Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ bool baseRetFlag = Bed3Interval::initFromFile(fileReader);
+
+ fileReader->getField(3, _name);
+ fileReader->getField(4, _score);
+ return baseRetFlag;
+}
+
+void Bed5Interval::print(QuickString &outBuf) const
+{
+ Bed3Interval::print(outBuf);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+}
+
+void Bed5Interval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+}
+
+void Bed5Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+}
+
+
+void Bed5Interval::printNull(QuickString &outBuf) const
+{
+ Bed3Interval::printNull(outBuf);
+ outBuf.append("\t.\t-1", 5);
+}
+
+const QuickString &Bed5Interval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 4:
+ return _name;
+ break;
+ case 5:
+ return _score;
+ break;
+
+ default:
+ return Bed3Interval::getField(fieldNum);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed5Interval.h b/src/utils/FileRecordTools/Records/Bed5Interval.h
new file mode 100644
index 0000000..bc913d1
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed5Interval.h
@@ -0,0 +1,36 @@
+/*
+ * Bed5Interval.h
+ *
+ * Created on: Nov 13, 2012
+ * Author: nek3d
+ */
+
+#ifndef BED5INTERVAL_H_
+#define BED5INTERVAL_H_
+
+
+#include "Bed3Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+class Bed5Interval : public Bed3Interval {
+public:
+ friend class FreeList<Bed5Interval>;
+
+ Bed5Interval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED5_RECORD_TYPE; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 5; }
+
+
+protected:
+ virtual ~Bed5Interval();
+};
+
+#endif /* BED5INTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.cpp b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
new file mode 100644
index 0000000..8371553
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed6Interval.cpp
@@ -0,0 +1,83 @@
+#include "Bed6Interval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstring>
+
+Bed6Interval::Bed6Interval()
+{
+
+}
+
+Bed6Interval::~Bed6Interval()
+{
+
+}
+
+bool Bed6Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ bool baseRetFlag = Bed3Interval::initFromFile(fileReader);
+
+ fileReader->getField(3, _name);
+ fileReader->getField(4, _score);
+ fileReader->getField(5, _strand);
+ adjustStrandVal();
+ return baseRetFlag;
+}
+
+void Bed6Interval::print(QuickString &outBuf) const
+{
+ Bed3Interval::print(outBuf);
+
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+ outBuf.append('\t');
+ outBuf.append(_strand);
+}
+
+void Bed6Interval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+ outBuf.append('\t');
+ outBuf.append(_strand);
+}
+
+void Bed6Interval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_score);
+ outBuf.append('\t');
+ outBuf.append(_strand);
+}
+
+
+void Bed6Interval::printNull(QuickString &outBuf) const
+{
+ Bed3Interval::printNull(outBuf);
+ outBuf.append("\t.\t-1\t.", 7);
+}
+
+const QuickString &Bed6Interval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 4:
+ return _name;
+ break;
+ case 5:
+ return _score;
+ break;
+ case 6:
+ return _strand;
+ break;
+ default:
+ return Bed3Interval::getField(fieldNum);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/Bed6Interval.h b/src/utils/FileRecordTools/Records/Bed6Interval.h
new file mode 100644
index 0000000..9ad9f80
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Bed6Interval.h
@@ -0,0 +1,36 @@
+/*
+ * Bed6Interval.h
+ *
+ * Created on: Nov 13, 2012
+ * Author: nek3d
+ */
+
+#ifndef BED6INTERVAL_H_
+#define BED6INTERVAL_H_
+
+
+#include "Bed3Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+class Bed6Interval : public Bed3Interval {
+public:
+ friend class FreeList<Bed6Interval>;
+
+ Bed6Interval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED6_RECORD_TYPE; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 6; }
+
+
+protected:
+ virtual ~Bed6Interval();
+};
+
+#endif /* BED6INTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.cpp b/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
new file mode 100644
index 0000000..e080857
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
@@ -0,0 +1,62 @@
+#include "BedGraphInterval.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstring>
+
+BedGraphInterval::BedGraphInterval()
+{
+
+}
+
+BedGraphInterval::~BedGraphInterval()
+{
+
+}
+
+bool BedGraphInterval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ bool baseRetFlag = Bed3Interval::initFromFile(fileReader);
+
+ fileReader->getField(3, _name);
+ return baseRetFlag;
+}
+
+void BedGraphInterval::print(QuickString &outBuf) const
+{
+ Bed3Interval::print(outBuf);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+void BedGraphInterval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+void BedGraphInterval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed3Interval::print(outBuf, start, end);
+ outBuf.append('\t');
+ outBuf.append(_name);
+}
+
+
+void BedGraphInterval::printNull(QuickString &outBuf) const
+{
+ Bed3Interval::printNull(outBuf);
+ outBuf.append("\t.", 2);
+}
+
+const QuickString &BedGraphInterval::getField(int fieldNum) const
+{
+ switch (fieldNum) {
+ case 4:
+ return _name;
+ break;
+ default:
+ return Bed3Interval::getField(fieldNum);
+ break;
+ }
+}
+
diff --git a/src/utils/FileRecordTools/Records/BedGraphInterval.h b/src/utils/FileRecordTools/Records/BedGraphInterval.h
new file mode 100644
index 0000000..1bdf619
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BedGraphInterval.h
@@ -0,0 +1,36 @@
+/*
+ * Bed6Interval.h
+ *
+ * Created on: Nov 13, 2012
+ * Author: nek3d
+ */
+
+#ifndef BEDGRAPHINTERVAL_H_
+#define BEDGRAPHINTERVAL_H_
+
+
+#include "Bed3Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+class BedGraphInterval : public Bed3Interval {
+public:
+ friend class FreeList<BedGraphInterval>;
+
+ BedGraphInterval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return 4; }
+
+
+protected:
+ virtual ~BedGraphInterval();
+};
+
+#endif /* BEDGRAPHINTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.cpp b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
new file mode 100644
index 0000000..fc8be36
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
@@ -0,0 +1,119 @@
+#include "BedPlusInterval.h"
+#include "SingleLineDelimTextFileReader.h"
+
+BedPlusInterval::BedPlusInterval()
+: _numPrintFields(0)
+{
+}
+
+BedPlusInterval::~BedPlusInterval()
+{
+ for (int i=0; i < (int)_otherIdxs.size(); i++) {
+ delete _otherIdxs[i];
+ }
+}
+
+const BedPlusInterval &BedPlusInterval::operator=(const BedPlusInterval &other) {
+ Bed6Interval::operator=(other);
+
+ int otherSize = other._otherIdxs.size();
+ int mySize = _otherIdxs.size();
+
+ _numPrintFields = other._numPrintFields;
+ int numMatchingFields = min(mySize, otherSize);
+ for (int i=0; i < numMatchingFields; i++) {
+ (*(_otherIdxs[i])) = (*(other._otherIdxs[i]));
+ }
+ if (mySize < otherSize) {
+ for (int i = mySize; i < otherSize; i++) {
+ QuickString *pqs = new QuickString(*(other._otherIdxs[i]));
+ _otherIdxs.push_back(pqs);
+ }
+ } else if (mySize > otherSize) {
+ for (int i= otherSize; i < mySize; i++) {
+ delete _otherIdxs[i];
+ }
+ _otherIdxs.resize(otherSize);
+ }
+ return *this;
+}
+
+bool BedPlusInterval::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ return (Bed6Interval::initFromFile(fileReader) && initOtherFieldsFromFile(fileReader));
+}
+
+bool BedPlusInterval::initOtherFieldsFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ int numFields = fileReader->getNumFields() - startOtherIdx;
+
+ if ((int)_otherIdxs.size() != numFields) {
+ if ((int)_otherIdxs.size() > 0) {
+ return false; //file had a number of fields not matching what was expected.
+ }
+ for (int i=0; i < numFields; i++) {
+ _otherIdxs.push_back(new QuickString());
+ }
+ }
+
+ for (int i=0; i < numFields; i++) {
+ fileReader->getField(i + startOtherIdx, (*(_otherIdxs[i])));
+ }
+ return true;
+}
+
+void BedPlusInterval::clear() {
+ Bed6Interval::clear();
+ _numPrintFields = 0;
+ for (int i=0; i < (int)_otherIdxs.size(); i++) {
+ _otherIdxs[i]->clear();
+ }
+}
+
+void BedPlusInterval::print(QuickString &outBuf) const
+{
+ Bed6Interval::print(outBuf);
+
+ for (int i=0; i < (int)_otherIdxs.size(); i++) {
+ outBuf.append('\t');
+ outBuf.append(*(_otherIdxs[i]));
+ }
+}
+
+void BedPlusInterval::print(QuickString &outBuf, int start, int end) const
+{
+ Bed6Interval::print(outBuf, start, end);
+ for (int i=0; i < (int)_otherIdxs.size(); i++) {
+ outBuf.append('\t');
+ outBuf.append(*(_otherIdxs[i]));
+ }
+}
+
+void BedPlusInterval::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ Bed6Interval::print(outBuf, start, end);
+ for (int i=0; i < (int)_otherIdxs.size(); i++) {
+ outBuf.append('\t');
+ outBuf.append(*(_otherIdxs[i]));
+ }
+}
+
+
+void BedPlusInterval::printNull(QuickString &outBuf) const
+{
+ Bed6Interval::printNull(outBuf);
+ for (int i=startOtherIdx; i < _numPrintFields; i++) {
+ outBuf.append("\t.");
+ }
+}
+
+const QuickString &BedPlusInterval::getField(int fieldNum) const
+{
+ //a request for any of the first six fields will retrieve
+ //chrom, start, end, name, score, and strand, in that order.
+ //A request for field 6+ will go to the otherIdxs.
+ if (fieldNum > startOtherIdx && fieldNum <= startOtherIdx + (int)_otherIdxs.size()) {
+ return (*(_otherIdxs[fieldNum - startOtherIdx - 1]));
+ }
+ return Bed6Interval::getField(fieldNum);
+}
diff --git a/src/utils/FileRecordTools/Records/BedPlusInterval.h b/src/utils/FileRecordTools/Records/BedPlusInterval.h
new file mode 100644
index 0000000..4b98b4f
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BedPlusInterval.h
@@ -0,0 +1,54 @@
+/*
+ * BedPlusInterval.h
+ *
+ * Created on: Nov 13, 2012
+ * Author: nek3d
+ */
+
+#ifndef BEDPLUSINTERVAL_H_
+#define BEDPLUSINTERVAL_H_
+
+#include "Bed6Interval.h"
+#include <vector>
+
+class SingleLineDelimTextFileReader;
+
+class BedPlusInterval : public Bed6Interval {
+public:
+ friend class FreeList<BedPlusInterval>;
+
+ BedPlusInterval();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void clear();
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED_PLUS_RECORD_TYPE; }
+
+ //Note: using the assignment operator in a BedPlusInterval can potentially be a performance hit,
+ //if the number of fields frequently differ between this object and the one being copied.
+ const BedPlusInterval &operator=(const BedPlusInterval &other);
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const { return startOtherIdx + _otherIdxs.size(); }
+
+ virtual void setField(int fieldNum, const QuickString &str) { (*(_otherIdxs[fieldNum])) = str; }
+ virtual void setField(int fieldNum, const string &str) { (*(_otherIdxs[fieldNum])) = str; }
+ virtual void setField(int fieldNum, const char *str) { (*(_otherIdxs[fieldNum])) = str; }
+ virtual void setNumPrintFields(int num) { _numPrintFields = num; }
+ virtual int getNumPrintFields() const { return _numPrintFields; }
+
+protected:
+ virtual ~BedPlusInterval();
+ bool initOtherFieldsFromFile(SingleLineDelimTextFileReader *fileReader);
+
+
+ vector<QuickString *> _otherIdxs;
+ static const int startOtherIdx = 6; //first six fields have names, and are not stored in otherIdxs.
+ int _numPrintFields;
+};
+
+
+
+#endif /* BEDPLUSINTERVAL_H_ */
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.cpp b/src/utils/FileRecordTools/Records/BlockMgr.cpp
new file mode 100644
index 0000000..21b060d
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BlockMgr.cpp
@@ -0,0 +1,217 @@
+/*
+ * BlockMgr.cpp
+ *
+ * Created on: May 14, 2013
+ * Author: nek3d
+ */
+
+#include "BlockMgr.h"
+#include "RecordMgr.h"
+#include "Bed12Interval.h"
+#include "BamRecord.h"
+#include "ParseTools.h"
+#include "api/BamAlignment.h"
+#include "api/BamAux.h"
+
+BlockMgr::BlockMgr(float overlapFraction, bool hasReciprocal)
+: _blockRecordsMgr(NULL),
+ _breakOnDeletionOps(false),
+ _breakOnSkipOps(true),
+ _overlapFraction(overlapFraction),
+ _hasReciprocal(hasReciprocal)
+{
+ _blockRecordsMgr = new RecordMgr(_blockRecordsType);
+}
+
+
+
+BlockMgr::~BlockMgr()
+{
+ delete _blockRecordsMgr;
+}
+
+void BlockMgr::getBlocks(RecordKeyList &keyList, bool &mustDelete)
+{
+ switch (keyList.getKey()->getType()) {
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ getBlocksFromBed12(keyList, mustDelete);
+ break; //not necessary after return, but here in case code is later modified.
+
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ getBlocksFromBam(keyList, mustDelete);
+ break;
+
+ default:
+ keyList.push_back(keyList.getKey());
+ mustDelete = false;
+ break;
+ }
+}
+
+
+
+void BlockMgr::getBlocksFromBed12(RecordKeyList &keyList, bool &mustDelete)
+{
+ const Bed12Interval *keyRecord = static_cast<const Bed12Interval *>(keyList.getKey());
+ int blockCount = keyRecord->getBlockCount();
+
+ if ( blockCount <= 0 ) {
+ mustDelete = false;
+ return;
+ }
+
+ vector<QuickString> sizes;
+ vector<QuickString> starts;
+
+ int sizeCount = Tokenize(keyRecord->getBlockSizes(), sizes, ',', blockCount);
+ int startCount = Tokenize(keyRecord->getBlockStarts(), starts, ',', blockCount);
+
+ if (blockCount != sizeCount || sizeCount != startCount) {
+ fprintf(stderr, "Error: found wrong block counts while splitting entry.\n");
+ exit(-1);
+ }
+
+ for (int i=0; i < blockCount; i++) {
+ int startPos = keyRecord->getStartPos() + str2chrPos(starts[i].c_str());
+ int endPos = startPos + str2chrPos(sizes[i].c_str());
+
+ const Record *record = allocateAndAssignRecord(keyRecord, startPos, endPos);
+ keyList.push_back(record);
+ }
+ mustDelete = true;
+}
+
+void BlockMgr::getBlocksFromBam(RecordKeyList &keyList, bool &mustDelete)
+{
+ const BamRecord *keyRecord = static_cast<const BamRecord *>(keyList.getKey());
+ const vector<BamTools::CigarOp> &cigarData = keyRecord->getAlignment().CigarData;
+
+ int currPos = keyRecord->getStartPos();
+ int blockLength = 0;
+
+ for (int i=0; i < (int)cigarData.size(); i++) {
+ char opType = cigarData[i].Type;
+ int opLen = (int)(cigarData[i].Length);
+
+ switch(opType) {
+ case 'I':
+ case 'S':
+ case 'P':
+ case 'H':
+ break;
+ case 'M':
+ blockLength += opLen;
+ break;
+ case 'D':
+ case 'N' :
+ if ((opType == 'D' && !_breakOnDeletionOps) ||
+ (opType == 'N' && !_breakOnSkipOps)) {
+ blockLength += opLen;
+ } else {
+ keyList.push_back(allocateAndAssignRecord(keyRecord, currPos, currPos + blockLength));
+ currPos += opLen + blockLength;
+ blockLength = 0;
+ }
+ break;
+ default:
+ fprintf(stderr, "ERROR: Found invalid Cigar operation: %c.\n", opType);
+ exit(1);
+ break;
+ }
+ }
+ if (blockLength > 0) {
+ keyList.push_back(allocateAndAssignRecord(keyRecord, currPos, currPos + blockLength));
+ }
+ mustDelete = true;
+}
+
+Record *BlockMgr::allocateAndAssignRecord(const Record *keyRecord, int startPos, int endPos)
+{
+ Record *record = _blockRecordsMgr->allocateRecord();
+ record->setChrName(keyRecord->getChrName());
+ record->setChromId(keyRecord->getChromId());
+ record->setStartPos(startPos);
+ record->setEndPos(endPos);
+ record->setName(keyRecord->getName());
+ record->setScore(keyRecord->getScore());
+ record->setStrand(keyRecord->getStrand());
+
+ return record;
+}
+
+int BlockMgr::getTotalBlockLength(RecordKeyList &keyList) {
+ int sum = 0;
+ for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ const Record *record = iter->value();
+ sum += record->getEndPos() - record->getStartPos();
+ }
+ return sum;
+}
+
+void BlockMgr::deleteBlocks(RecordKeyList &keyList)
+{
+ for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ _blockRecordsMgr->deleteRecord(iter->value());
+ }
+ keyList.clearList();
+
+}
+
+
+int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList, RecordKeyList &resultList)
+{
+ bool deleteKeyBlocks = false;
+ if (keyList.empty()) {
+ //get all the blocks for the query record, put them in it's list.
+ getBlocks(keyList, deleteKeyBlocks);
+ }
+ _overlapBases.clear();
+ int keyBlocksSumLength = getTotalBlockLength(keyList);
+ //Loop through every database record the query intersected with
+ for (RecordKeyList::const_iterator_type hitListIter = hitList.begin(); hitListIter != hitList.end(); hitListIter = hitList.next()) {
+ RecordKeyList hitBlocks(hitListIter->value());
+ bool deleteHitBlocks = false;
+ getBlocks(hitBlocks, deleteHitBlocks); //get all blocks for the hit record.
+ int hitBlockSumLength = getTotalBlockLength(hitBlocks); //get total lentgh of the bocks for the hitRecord.
+ int totalHitOverlap = 0;
+ bool hitHasOverlap = false;
+
+ //loop through every block of the database record.
+ for (RecordKeyList::const_iterator_type hitBlockIter = hitBlocks.begin(); hitBlockIter != hitBlocks.end(); hitBlockIter = hitBlocks.next()) {
+ //loop through every block of the query record.
+ for (RecordKeyList::const_iterator_type keyListIter = keyList.begin(); keyListIter != keyList.end(); keyListIter = keyList.next()) {
+ const Record *keyBlock = keyListIter->value();
+ const Record *hitBlock = hitBlockIter->value();
+
+ int maxStart = max(keyBlock->getStartPos(), hitBlock->getStartPos());
+ int minEnd = min(keyBlock->getEndPos(), hitBlock->getEndPos());
+ int overlap = minEnd - maxStart;
+ if (overlap > 0) {
+ hitHasOverlap = true;
+ totalHitOverlap += overlap;
+ }
+
+ }
+ }
+ _overlapBases.push_back(totalHitOverlap);
+ if (hitHasOverlap) {
+ if ((float) totalHitOverlap / (float)keyBlocksSumLength > _overlapFraction) {
+ if (_hasReciprocal &&
+ ((float)totalHitOverlap / (float)hitBlockSumLength > _overlapFraction)) {
+ resultList.push_back(hitListIter->value());
+ } else if (!_hasReciprocal) {
+ resultList.push_back(hitListIter->value());
+ }
+ }
+ }
+ if (deleteHitBlocks) {
+ deleteBlocks(hitBlocks);
+ }
+ }
+ if (deleteKeyBlocks) {
+ deleteBlocks(keyList);
+ }
+ resultList.setKey(keyList.getKey());
+ return (int)resultList.size();
+}
+
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.h b/src/utils/FileRecordTools/Records/BlockMgr.h
new file mode 100644
index 0000000..c83b1e0
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/BlockMgr.h
@@ -0,0 +1,65 @@
+/*
+ * BlockMgr.h
+ *
+ * Created on: May 14, 2013
+ * Author: nek3d
+ */
+
+#ifndef BLOCKMGR_H_
+#define BLOCKMGR_H_
+
+//This class handles blocks inside of a larger record, such as BED12 and BAM records.
+//Produce and manage seperate records for the sub-intervals inside the
+
+using namespace std;
+
+#include "FileRecordTypeChecker.h"
+#include "RecordKeyList.h"
+
+class RecordMgr;
+
+class BlockMgr {
+public:
+ BlockMgr(float overlapFraction = 1E-9, bool hasReciprocal = false);
+ ~BlockMgr();
+
+ // Return value is the number of blocks this main record has been split into.
+ void getBlocks(RecordKeyList &keyList, bool &mustDelete);
+ void deleteBlocks(RecordKeyList &keyList);
+
+ // Get the sum of the lengths of all blocks for a record.
+ int getTotalBlockLength(RecordKeyList &keyList);
+
+ // Determine which hits in the hitList intersect the hits in the keyList by comparing all blocks in each
+ // and checking that their total intersection meets any overlapFraction and reciprocal criteria compared to
+ // the total block lengths of the hitList and keyList. All hits that pass will be in the resultList.
+ // Return value is the number of hits in the result set.
+
+ int findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList, RecordKeyList &resultList);
+
+ //these are setting options for splitting BAM records
+ void setBreakOnDeletionOps(bool val) { _breakOnDeletionOps = val; }
+ void setBreakOnSkipOps(bool val) { _breakOnSkipOps = val; }
+ int getOverlapBases(int hitIdx) const { return _overlapBases[hitIdx]; }
+
+private:
+ RecordMgr *_blockRecordsMgr;
+ bool _breakOnDeletionOps;
+ bool _breakOnSkipOps;
+ vector<int> _overlapBases;
+
+ float _overlapFraction;
+ bool _hasReciprocal;
+
+ // For now, all records will be split into Bed6 records.
+ const static FileRecordTypeChecker::RECORD_TYPE _blockRecordsType = FileRecordTypeChecker::BED6_RECORD_TYPE;
+ void getBlocksFromBed12(RecordKeyList &keyList, bool &mustDelete);
+ void getBlocksFromBam(RecordKeyList &keyList, bool &mustDelete);
+
+ Record *allocateAndAssignRecord(const Record *keyRecord, int startPos, int endPos);
+
+
+};
+
+
+#endif /* BLOCKMGR_H_ */
diff --git a/src/utils/FileRecordTools/Records/GffRecord.cpp b/src/utils/FileRecordTools/Records/GffRecord.cpp
new file mode 100644
index 0000000..a91ce15
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/GffRecord.cpp
@@ -0,0 +1,159 @@
+#include "GffRecord.h"
+#include "SingleLineDelimTextFileReader.h"
+#include <cstring>
+
+GffRecord::GffRecord()
+{
+
+}
+
+GffRecord::~GffRecord()
+{
+
+}
+
+void GffRecord::clear()
+{
+ Bed6Interval::clear();
+ _source.clear();
+ _frame.clear();
+ _group.clear();
+ _numFields = 8;
+}
+
+bool GffRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ fileReader->getField(0, _chrName);
+ fileReader->getField(3, _startPosStr);
+ _startPos = str2chrPos(_startPosStr);
+ _startPos--; // VCF is one-based. Here we intentionally don't decrement the string version,
+ //because we'll still want to output the one-based number in the print methods, even though
+ //internally we decrement the integer to comply with the 0-based format common to other records.
+ fileReader->getField(4, _endPosStr);
+ //endPos is just the startPos plus the length of the variant
+ _endPos = str2chrPos(_endPosStr);
+
+ fileReader->getField(2, _name);
+ fileReader->getField(1, _source);
+ fileReader->getField(5, _score);
+
+ //GFF allows a '.' for the strandChar, signifying it is not known.
+ fileReader->getField(6, _strand);
+ adjustStrandVal();
+
+ fileReader->getField(7, _frame);
+ _numFields = fileReader->getNumFields();
+ if (_numFields == 9) {
+ fileReader->getField(8, _group);
+ }
+
+
+ return true;
+}
+
+void GffRecord::print(QuickString &outBuf) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_source);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_startPosStr);
+ outBuf.append('\t');
+ outBuf.append(_endPosStr);
+ outBuf.append('\t');
+
+ printRemainingFields(outBuf);
+}
+
+void GffRecord::print(QuickString &outBuf, int start, int end) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_source);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(start +1);
+ outBuf.append('\t');
+ outBuf.append(end);
+ outBuf.append('\t');
+
+ printRemainingFields(outBuf);
+}
+
+void GffRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const
+{
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_source);
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(start);
+ outBuf.append('\t');
+ outBuf.append(end);
+ outBuf.append('\t');
+
+ printRemainingFields(outBuf);
+}
+
+void GffRecord::printRemainingFields(QuickString &outBuf) const
+{
+ outBuf.append(_score);
+ outBuf.append('\t');
+ outBuf.append(_strand);
+ outBuf.append('\t');
+ outBuf.append(_frame);
+ if (_numFields == 9) {
+ outBuf.append('\t');
+ outBuf.append(_group);
+ }
+}
+
+void GffRecord::printNull(QuickString &outBuf) const
+{
+ outBuf.append(".\t.\t.\t-1\t-1\t.\t.\t.", 17);
+ if (_numFields > 8) {
+ outBuf.append("\t.", 2);
+ }
+}
+
+const QuickString &GffRecord::getField(int fieldNum) const
+{
+ if (fieldNum == 9 && _numFields == 9) {
+ return _group;
+ }
+ switch (fieldNum) {
+ case 1:
+ return _chrName;
+ break;
+ case 2:
+ return _source;
+ break;
+ case 3:
+ return _name;
+ break;
+ case 4:
+ return _startPosStr;
+ break;
+ case 5:
+ return _endPosStr;
+ break;
+ case 6:
+ return _score;
+ break;
+ case 7:
+ return _strand;
+ break;
+ case 8:
+ return _frame;
+ break;
+ default:
+ return Bed6Interval::getField(fieldNum);
+ break;
+ }
+}
+
+
diff --git a/src/utils/FileRecordTools/Records/GffRecord.h b/src/utils/FileRecordTools/Records/GffRecord.h
new file mode 100644
index 0000000..b84d96a
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/GffRecord.h
@@ -0,0 +1,51 @@
+/*
+ * GffRecord.h
+ *
+ * Created on: Nov 13, 2012
+ * Author: nek3d
+ */
+
+#ifndef GFF_RECORD_H_
+#define GFF_RECORD_H_
+
+#include "Bed6Interval.h"
+
+class SingleLineDelimTextFileReader;
+
+class GffRecord : public Bed6Interval {
+public:
+ friend class FreeList<GffRecord>;
+
+ GffRecord();
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void clear();
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BED_PLUS_RECORD_TYPE; }
+ virtual const QuickString &getSource() const { return _source; }
+ virtual const QuickString &getFrame() const { return _frame; }
+ virtual const QuickString &getGroup() const { return _group; }
+ virtual int getNumFields() const { return _numFields; }
+ virtual void setNumFields(int val) { _numFields = val; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ //Note: using the assignment operator in a GffRecord can potentially be a performance hit,
+ //if the number of fields frequently differ between this object and the one being copied.
+ const GffRecord &operator=(const GffRecord &other);
+
+protected:
+ virtual ~GffRecord();
+ void printRemainingFields(QuickString &outbuf) const;
+
+ int _numFields;
+ QuickString _source;
+ QuickString _frame;
+ QuickString _group;
+
+};
+
+
+
+#endif /* GFF_RECORD_H_ */
diff --git a/src/utils/FileRecordTools/Records/Makefile b/src/utils/FileRecordTools/Records/Makefile
new file mode 100644
index 0000000..6bfd610
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Makefile
@@ -0,0 +1,45 @@
+OBJ_DIR = ../../../../obj/
+BIN_DIR = ../../../../bin/
+UTILITIES_DIR = ../../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= RecordMgr.cpp RecordMgr.h Record.h Record.cpp Bed3Interval.h Bed3Interval.cpp \
+ Bed4Interval.h Bed4Interval.cpp BedGraphInterval.h BedGraphInterval.cpp Bed5Interval.h Bed5Interval.cpp \
+ Bed6Interval.h Bed6Interval.cpp \
+ BedPlusInterval.h BedPlusInterval.cpp Bed12Interval.h Bed12Interval.cpp BamRecord.h BamRecord.cpp VcfRecord.h VcfRecord.cpp \
+ GffRecord.h GffRecord.cpp RecordKeyList.h RecordKeyList.cpp BlockMgr.h BlockMgr.cpp
+OBJECTS= RecordMgr.o Record.o Bed3Interval.o Bed4Interval.o BedGraphInterval.o Bed5Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
+ VcfRecord.o GffRecord.o RecordKeyList.o BlockMgr.o
+_EXT_OBJECTS=ParseTools.o QuickString.o ChromIdLookup.o
+EXT_OBJECTS=$(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)/RecordMgr.o $(OBJ_DIR)/Record.o $(OBJ_DIR)/Bed3Interval.o $(OBJ_DIR)/Bed4Interval.o \
+ $(OBJ_DIR)/BedGraphInterval.o $(OBJ_DIR)/Bed5Interval.o $(OBJ_DIR)/Bed6Interval.o \
+ $(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
new file mode 100644
index 0000000..2beb4dc
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -0,0 +1,203 @@
+
+#include "Record.h"
+#include <cstdio>
+
+Record::Record()
+: _chrId(-1),
+ _startPos(-1),
+ _endPos(-1),
+ _strandVal(UNKNOWN),
+ _zeroLength(false),
+ _isUnmapped(false),
+ _isMateUnmapped(false)
+{
+}
+
+Record::~Record() {
+}
+
+const Record &Record::operator=(const Record &other)
+{
+ _chrName = other._chrName;
+ _chrId = other._chrId;
+ _startPos = other._startPos;
+ _endPos = other._endPos;
+ _strand = other._strand;
+ _strandVal = other._strandVal;
+ _name = other._name;
+ return *this;
+}
+
+void Record::clear() {
+ _chrName.clear();
+ _chrId = -1;
+ _startPos = -1;
+ _endPos = -1;
+ _name.clear();
+ _score.clear();
+ _strand.clear();
+ _strandVal = UNKNOWN;
+ _startPosStr.clear();
+ _endPosStr.clear();
+ _zeroLength = false;
+ _isUnmapped = false;
+ _isMateUnmapped = false;
+}
+
+bool Record::operator < (const Record &other) const
+{
+
+ if (!sameChrom(&other)) {
+ return chromBefore(&other);
+ }
+ if (_startPos != other._startPos) {
+ return _startPos < other._startPos;
+ }
+ if (_endPos != other._endPos) {
+ return _endPos < other._endPos;
+ }
+ return false;
+}
+
+bool Record::operator > (const Record &other) const {
+ if (!sameChrom(&other)) {
+ return chromAfter(&other);
+ }
+ if (_startPos != other._startPos) {
+ return _startPos > other._startPos;
+ }
+ if (_endPos != other._endPos) {
+ return _endPos > other._endPos;
+ }
+ return false;
+}
+
+bool Record::sameChrom(const Record *other) const {
+ return (_chrId == -1 || other->_chrId == -1) ? ( _chrName == other->_chrName) : (_chrId == other->_chrId);
+}
+
+bool Record::chromBefore(const Record *other) const
+{
+ return (_chrId == -1 || other->_chrId == -1) ? ( _chrName < other->_chrName) : (_chrId < other->_chrId);
+}
+
+bool Record::chromAfter(const Record *other) const
+{
+ return (_chrId == -1 || other->_chrId == -1) ? ( _chrName > other->_chrName) : (_chrId > other->_chrId);
+}
+
+
+
+bool Record::after(const Record *other) const
+{
+ return (_chrId == other->_chrId && _startPos >= other->_endPos);
+}
+
+bool Record::intersects(const Record *record,
+ bool wantSameStrand, bool wantDiffStrand, float overlapFraction, bool reciprocal) const
+{
+ //must be on same chromosome
+ if (!sameChrom(record)) {
+ return false;
+ }
+ return sameChromIntersects(record, wantSameStrand, wantDiffStrand, overlapFraction, reciprocal);
+}
+
+bool Record::sameChromIntersects(const Record *record,
+ bool wantSameStrand, bool wantDiffStrand, float overlapFraction, bool reciprocal) const
+{
+ // Special: For records that are unmapped, intersect should automatically return false
+ if (_isUnmapped || record->isUnmapped()) {
+ return false;
+ }
+
+ //If user requested hits only on same strand, or only on different strands,
+ //rule out different strandedness first.
+ //If the strand is unknown in either case, then queries regarding strandedness
+ //can not be answered, so we return false;
+ bool isSameStrand = (_strandVal == record->_strandVal && _strandVal != UNKNOWN);
+ bool isDiffStrand = ( _strandVal != UNKNOWN && record->_strandVal != UNKNOWN && _strandVal != record->_strandVal);
+
+ if (wantSameStrand && !isSameStrand) {
+ return false; //want same, but they're not same.
+ }
+ if (wantDiffStrand && !isDiffStrand) {
+ return false; //want different, but they're not different.
+ }
+
+ int otherStart = record->getStartPos();
+ int otherEnd = record->getEndPos();
+
+ int maxStart = max(_startPos, otherStart);
+ int minEnd = min(_endPos, otherEnd);
+
+ //rule out all cases of no intersection at all
+ if (minEnd < maxStart) {
+ return false;
+ }
+
+
+ int overlapBases = minEnd - maxStart;
+ int len = _endPos - _startPos;
+ int otherLen = otherEnd - otherStart;
+
+ if ((float)overlapBases / (float)len < overlapFraction) {
+ return false;
+ }
+
+ //at this point, we've ruled out strandedness, non-intersection,
+ //and query coverage (overlapFraction). The only thing left is
+ //database coverage.
+ if (!reciprocal) {
+ return true;
+ }
+
+ if ((float)overlapBases / (float)otherLen >= overlapFraction) {
+ return true;
+ }
+
+ return false;
+}
+
+bool Record::coordsValid() {
+ if (_startPos < 0 || _endPos < 0 || _endPos < _startPos) {
+ return false;
+ }
+ adjustZeroLength();
+ return true;
+}
+
+void Record::adjustZeroLength()
+{
+ if (_startPos == _endPos) {
+ _zeroLength = true;
+ _startPos--;
+ _endPos++;
+ }
+}
+
+void Record::undoZeroLength()
+{
+ if (_zeroLength) {
+ _startPos++;
+ _endPos--;
+ _zeroLength = false;
+ }
+}
+
+ostream &operator << (ostream &out, const Record &record)
+{
+ QuickString errBuf;
+ record.print(errBuf);
+ out << errBuf;
+ return out;
+}
+
+const QuickString &Record::getField(int fieldNum) const
+{
+ cerr << endl << "*****" << endl
+ << "*****ERROR: requested column " << fieldNum <<
+ " , but record only has fields 1 - " << getNumFields() << ". Exiting." << endl
+ << endl << "*****" << endl;
+ exit(1);
+}
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
new file mode 100644
index 0000000..2c303d9
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -0,0 +1,155 @@
+/*
+ * Record.h
+ *
+ * Created on: Nov 8, 2012
+ * Author: nek3d
+ */
+
+using namespace std;
+
+#ifndef RECORD_H_
+#define RECORD_H_
+
+#include "FreeList.h"
+#include "QuickString.h"
+#include "FileRecordTypeChecker.h"
+
+class FileRecordMgr;
+class FileReader;
+class ChromIdLookup;
+
+class Record {
+public:
+ friend class RecordMgr;
+ friend class RecordOutputMgr;
+
+ friend class FreeList<Record>;
+
+ typedef enum { FORWARD, REVERSE, UNKNOWN } strandType;
+ Record();
+ virtual bool initFromFile(FileReader *) =0;
+ virtual void clear();
+ virtual void print(QuickString &outBuf) const {}
+ virtual void print(QuickString &outBuf, int start, int end) const {}
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const {}
+ virtual void printNull(QuickString &outBuf) const {}
+ friend ostream &operator << (ostream &out, const Record &record);
+
+ virtual const Record & operator=(const Record &);
+
+ virtual const QuickString &getChrName() const { return _chrName; }
+ virtual void setChrName(const QuickString &chr) { _chrName = chr; }
+ virtual void setChrName(const string &chr) { _chrName = chr; }
+ virtual void setChrName(const char *chr) { _chrName = chr; }
+
+
+ virtual int getChromId() const { return _chrId; }
+ virtual void setChromId(int id) { _chrId = id; }
+
+ virtual int getStartPos() const { return _startPos; }
+ virtual void setStartPos(int startPos) { _startPos = startPos; }
+ virtual const QuickString &getStartPosStr() const { return _startPosStr; }
+ virtual void setStartPosStr(const QuickString &str) { _startPosStr = str; }
+
+ virtual int getEndPos() const { return _endPos; }
+ virtual void setEndPos(int endPos) { _endPos = endPos; }
+ virtual const QuickString &getEndPosStr() const { return _endPosStr; }
+ virtual void setEndPosStr(const QuickString &str) { _endPosStr = str; }
+
+ virtual bool getZeroLength() const { return _zeroLength; }
+ virtual void setZeroLength(bool val) { _zeroLength = val; }
+
+ virtual const QuickString &getStrand() const { return _strand; }
+ virtual void setStrand(const QuickString &val) { _strand = val;
+ _strandVal = (val == "+" ? FORWARD : (val == "-" ? REVERSE : UNKNOWN));
+ }
+ virtual void setStrand(char val) { _strand = val;
+ _strandVal = (val == '+' ? FORWARD : (val == '-' ? REVERSE : UNKNOWN));
+ }
+ virtual void adjustStrandVal() {
+ _strandVal = (_strand == "+" ? FORWARD : (_strand == "-" ? REVERSE : UNKNOWN));
+ }
+
+ virtual strandType getStrandVal() const {return _strandVal; }
+
+ virtual const QuickString &getName() const { return _name; }
+ virtual void setName(const QuickString &chr) { _name = chr; }
+ virtual void setName(const string &chr) { _name = chr; }
+ virtual void setName(const char *chr) { _name = chr; }
+
+ virtual const QuickString &getScore() const { return _score; }
+ virtual void setScore(const QuickString &chr) { _score = chr; }
+ virtual void setScore(const string &chr) { _score = chr; }
+ virtual void setScore(const char *chr) { _score = chr; }
+
+ virtual const QuickString &getField(int fieldNum) const;
+ virtual int getNumFields() const = 0;
+
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::UNKNOWN_RECORD_TYPE; }
+
+ virtual bool coordsValid(); //test that no coords negative, end not less than start, check zeroLength (see below).
+
+ //Some files can have insertions of the form 2,2. If found this should translate to cover the base before and after,
+ //thus meaning the startPos is decremented and the endPos is incremented. This method will find and handle that case.
+ //Don't adjust the startPosStr and endPosStr strings because they aren't used in
+ //calculation. They're only used in output, and it would be slower to change them
+ //and then change them back.
+ virtual void adjustZeroLength();
+ virtual void undoZeroLength(); //change it back just before output;
+ virtual bool isZeroLength() const { return _zeroLength; }
+
+ // "Unmapped" only applies to BamRecord, but for design reasons, it has to be here,
+ // because we want to short circuit the intersects method if either record is an unmapped
+ // Bam record.
+ bool isUnmapped() const { return _isUnmapped; }
+ bool isMateUnmapped() const { return _isMateUnmapped; }
+ virtual void printUnmapped(QuickString &outBuf) const {}
+
+
+
+ virtual bool operator < (const Record &other) const;
+ virtual bool operator > (const Record &other) const;
+
+
+ //is this on the same chromosome as another record?
+ bool sameChrom(const Record *other) const;
+ bool chromBefore(const Record *other) const;
+ bool chromAfter(const Record *other) const;
+
+ //is this record after the other one?
+ virtual bool after(const Record *other) const;
+
+ //does this record intersect with another record?
+ virtual bool intersects(const Record *otherRecord,
+ bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal) const;
+
+ // *** WARNING !!! ** sameChromIntersects is a faster version of the intersects method,
+ // BUT the caller MUST ensure that the records are on the same
+ //chromosome. If you're not absolutely sure, use the regular intersects method.
+ virtual bool sameChromIntersects(const Record *otherRecord,
+ bool sameStrand, bool diffStrand, float overlapFraction, bool reciprocal) const;
+
+
+protected:
+ virtual ~Record(); //by making the destructor protected, only the friend class(es) can actually delete Record objects, or objects derived from Record.
+
+ QuickString _chrName;
+ int _chrId;
+ int _startPos;
+ int _endPos;
+ //It is actually faster to also store the start and end positions as their original strings than to
+ //have to convert their integer representations back to strings when printing them.
+ QuickString _startPosStr;
+ QuickString _endPosStr;
+ QuickString _name;
+ QuickString _score;
+ QuickString _strand;
+ strandType _strandVal;
+ bool _zeroLength;
+ bool _isUnmapped;
+ bool _isMateUnmapped;
+};
+
+
+
+#endif /* RECORD_H_ */
diff --git a/src/utils/FileRecordTools/Records/RecordKeyList.cpp b/src/utils/FileRecordTools/Records/RecordKeyList.cpp
new file mode 100644
index 0000000..6f25dac
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordKeyList.cpp
@@ -0,0 +1,68 @@
+#include "RecordKeyList.h"
+
+RecordKeyList::RecordKeyList()
+: _key(NULL)
+{
+}
+
+RecordKeyList::RecordKeyList(const Record * item)
+: _key(item)
+{
+}
+
+RecordKeyList::RecordKeyList(const Record * item, const listType &list)
+: _key(item)
+{
+ _list = list;
+}
+
+RecordKeyList::~RecordKeyList() {
+}
+
+const RecordKeyList &RecordKeyList::operator=(const RecordKeyList &other)
+{
+ setKey(other._key);
+ _list = other._list;
+ return *this;
+}
+
+const RecordKeyList::const_iterator_type RecordKeyList::begin() {
+ return _list.begin();
+}
+
+const RecordKeyList::const_iterator_type RecordKeyList::next() {
+ return _list.next();
+}
+
+
+const RecordKeyList::const_iterator_type RecordKeyList::end() {
+ return _list.end();
+}
+
+size_t RecordKeyList::size() const {
+ return _list.size();
+}
+
+bool RecordKeyList::empty() const {
+ return _list.empty();
+}
+
+void RecordKeyList::push_back(elemType item) {
+ _list.push_back(item);
+}
+
+const Record *RecordKeyList::getKey() const {
+ return _key;
+}
+
+void RecordKeyList::setKey(elemType key) {
+ _key = key;
+}
+
+void RecordKeyList::setListNoCopy(listType &list) {
+ _list.assignNoCopy(list);
+}
+
+void RecordKeyList::clearList() {
+ _list.clear();
+}
diff --git a/src/utils/FileRecordTools/Records/RecordKeyList.h b/src/utils/FileRecordTools/Records/RecordKeyList.h
new file mode 100644
index 0000000..f5d1251
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordKeyList.h
@@ -0,0 +1,60 @@
+/*
+ * RecordKeyList.h
+ *
+ * Created on: Dec 14, 2012
+ * Author: nek3d
+ */
+
+#ifndef KEYLIST_H_
+#define KEYLIST_H_
+
+
+
+
+using namespace std;
+
+#include "Record.h"
+#include "BTlist.h"
+
+class RecordKeyList {
+public:
+ typedef const Record * elemType;
+ typedef BTlist<elemType> listType;
+ typedef const BTlistNode<elemType> *const_iterator_type;
+ RecordKeyList();
+ RecordKeyList(elemType item);
+ RecordKeyList(elemType item, const listType &list);
+ ~RecordKeyList();
+
+ const RecordKeyList &operator=(const RecordKeyList &other);
+ const const_iterator_type begin();
+ const const_iterator_type next();
+ const const_iterator_type end();
+ size_t size() const ;
+ bool empty() const ; //only checks whether list is empty. Doesn't check key.
+ void push_back(elemType item);
+ elemType getKey() const ;
+ void setKey(elemType key);
+
+ //setListNoCopy will make our list share the nodes of another
+ //list, not copy them.
+ void setListNoCopy(listType &list);
+
+ // WARNING! clearList will NOT delete records pointed to by list nodes. Caller must do that separately, since the RecordKeyList
+ // does not have it's own RecordMgr member.
+ void clearList();
+
+ void clearAll() {
+ setKey(NULL);
+ clearList();
+ }
+ bool allClear() { return (_key == NULL && empty()); }
+
+
+private:
+ elemType _key;
+ listType _list;
+};
+
+
+#endif /* RECORDKEYLIST_H_ */
diff --git a/src/utils/FileRecordTools/Records/RecordMgr.cpp b/src/utils/FileRecordTools/Records/RecordMgr.cpp
new file mode 100644
index 0000000..9799fed
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordMgr.cpp
@@ -0,0 +1,277 @@
+#include "RecordMgr.h"
+
+#include "FreeList.h"
+
+RecordMgr::RecordMgr(FileRecordTypeChecker::RECORD_TYPE recType, int blockSize)
+: _recordType(recType),
+ _freeList(NULL),
+ _freeListBlockSize(blockSize)
+{
+ switch(_recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ {
+ _freeList = new FreeList<Bed3Interval>(_freeListBlockSize);
+ break;
+ }
+
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ {
+ _freeList = new FreeList<Bed4Interval>(_freeListBlockSize);
+ break;
+ }
+
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ {
+ _freeList = new FreeList<Bed5Interval>(_freeListBlockSize);
+ break;
+ }
+
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ {
+ _freeList = new FreeList<BedGraphInterval>(_freeListBlockSize);
+ break;
+ }
+
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ {
+ _freeList = new FreeList<Bed6Interval>(_freeListBlockSize);
+ break;
+ }
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ {
+ _freeList = new FreeList<BedPlusInterval>(_freeListBlockSize);
+ break;
+ }
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ {
+ _freeList = new FreeList<Bed12Interval>(_freeListBlockSize);
+ break;
+ }
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ {
+ _freeList = new FreeList<BamRecord>(_freeListBlockSize);
+ break;
+ }
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ {
+ _freeList = new FreeList<VcfRecord>(_freeListBlockSize);
+ break;
+ }
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ {
+ _freeList = new FreeList<GffRecord>(_freeListBlockSize);
+ break;
+ }
+
+
+ default:
+ break;
+ }
+}
+
+RecordMgr::~RecordMgr()
+{
+ switch(_recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ {
+ delete (FreeList<Bed3Interval> *)_freeList;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ {
+ delete (FreeList<Bed4Interval> *)_freeList;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ {
+ delete (FreeList<Bed5Interval> *)_freeList;
+ break;
+ }
+
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ {
+ delete (FreeList<BedGraphInterval> *)_freeList;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ {
+ delete (FreeList<Bed6Interval> *)_freeList;
+ break;
+ }
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ {
+ delete (FreeList<BedPlusInterval> *)_freeList;
+ break;
+ }
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ {
+ delete (FreeList<Bed12Interval> *)_freeList;
+ break;
+ }
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ {
+ delete (FreeList<BamRecord> *)_freeList;
+ break;
+ }
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ {
+ delete (FreeList<VcfRecord> *)_freeList;
+ break;
+ }
+
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ {
+ delete (FreeList<GffRecord> *)_freeList;
+ break;
+ }
+
+
+ default:
+ break;
+ }
+}
+
+Record *RecordMgr::allocateRecord()
+{
+ Record *record = NULL;
+ switch(_recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ {
+ Bed3Interval *b3i = ((FreeList<Bed3Interval> *)_freeList)->newObj();
+ record = b3i;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ {
+ Bed4Interval *b4i = ((FreeList<Bed4Interval> *)_freeList)->newObj();
+ record = b4i;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ {
+ Bed5Interval *b5i = ((FreeList<Bed5Interval> *)_freeList)->newObj();
+ record = b5i;
+ break;
+ }
+
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ {
+ BedGraphInterval *bgi = ((FreeList<BedGraphInterval> *)_freeList)->newObj();
+ record = bgi;
+ break;
+ }
+
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ {
+ Bed6Interval *b6i = ((FreeList<Bed6Interval> *)_freeList)->newObj();
+ record = b6i;
+ break;
+ }
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ {
+ BedPlusInterval *bPi = ((FreeList<BedPlusInterval> *)_freeList)->newObj();
+ record = bPi;
+ break;
+ }
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ {
+ Bed12Interval *b12i = ((FreeList<Bed12Interval> *)_freeList)->newObj();
+ record = b12i;
+ break;
+ }
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ {
+ BamRecord *bamRec = ((FreeList<BamRecord> *)_freeList)->newObj();
+ record = bamRec;
+ break;
+ }
+
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ {
+ VcfRecord *vcfRec = ((FreeList<VcfRecord> *)_freeList)->newObj();
+ record = vcfRec;
+ break;
+ }
+
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ {
+ GffRecord *gfr = ((FreeList<GffRecord> *)_freeList)->newObj();
+ record = gfr;
+ break;
+ }
+
+
+ default:
+ break;
+ }
+ return record;
+}
+
+void RecordMgr::deleteRecord(const Record *record)
+{
+ switch(_recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ {
+ ((FreeList<Bed3Interval> *)_freeList)->deleteObj(static_cast<const Bed3Interval *>(record));
+ break;
+ }
+
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ {
+ ((FreeList<Bed4Interval> *)_freeList)->deleteObj(static_cast<const Bed4Interval *>(record));
+ break;
+ }
+
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ {
+ ((FreeList<Bed5Interval> *)_freeList)->deleteObj(static_cast<const Bed5Interval *>(record));
+ break;
+ }
+
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ {
+ ((FreeList<BedGraphInterval> *)_freeList)->deleteObj(static_cast<const BedGraphInterval *>(record));
+ break;
+ }
+
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ {
+ ((FreeList<Bed6Interval> *)_freeList)->deleteObj(static_cast<const Bed6Interval *>(record));
+ break;
+ }
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ {
+ ((FreeList<BedPlusInterval> *)_freeList)->deleteObj(static_cast<const BedPlusInterval *>(record));
+ break;
+ }
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ {
+ ((FreeList<Bed12Interval> *)_freeList)->deleteObj(static_cast<const Bed12Interval *>(record));
+ break;
+ }
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ {
+ ((FreeList<BamRecord> *)_freeList)->deleteObj(static_cast<const BamRecord *>(record));
+ break;
+ }
+
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ {
+ ((FreeList<VcfRecord> *)_freeList)->deleteObj(static_cast<const VcfRecord *>(record));
+ break;
+ }
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ {
+ ((FreeList<GffRecord> *)_freeList)->deleteObj(static_cast<const GffRecord *>(record));
+ break;
+ }
+
+ default:
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/RecordMgr.h b/src/utils/FileRecordTools/Records/RecordMgr.h
new file mode 100644
index 0000000..1d73f90
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordMgr.h
@@ -0,0 +1,47 @@
+/*
+ * RecordMgr.h
+ *
+ * Created on: Jan 9, 2013
+ * Author: nek3d
+ */
+
+#ifndef RECORDMGR_H_
+#define RECORDMGR_H_
+
+//include headers for all Records and derivative classes
+#include "Record.h"
+#include "Bed3Interval.h"
+#include "Bed4Interval.h"
+#include "Bed5Interval.h"
+#include "BedGraphInterval.h"
+#include "Bed6Interval.h"
+#include "BedPlusInterval.h"
+#include "Bed12Interval.h"
+#include "BamRecord.h"
+#include "VcfRecord.h"
+#include "GffRecord.h"
+
+#include "FileRecordTypeChecker.h"
+
+class Record;
+
+class RecordMgr {
+public:
+ RecordMgr(FileRecordTypeChecker::RECORD_TYPE recType, int blockSize = 512);
+ ~RecordMgr();
+
+ Record *allocateRecord();
+
+ //WARNING: Even though the deleteRecord method takes a const pointer, user should only pass objects
+ //that are safe to delete! Const-ness will be cast away internally.
+ void deleteRecord(const Record *);
+
+private:
+ FileRecordTypeChecker::RECORD_TYPE _recordType;
+ void *_freeList;
+ int _freeListBlockSize;
+};
+
+
+
+#endif /* RECORDMGR_H_ */
diff --git a/src/utils/FileRecordTools/Records/VcfRecord.cpp b/src/utils/FileRecordTools/Records/VcfRecord.cpp
new file mode 100644
index 0000000..20cbb6f
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/VcfRecord.cpp
@@ -0,0 +1,111 @@
+/*
+ * VcfRecord.cpp
+ *
+ * Created on: May 1, 2013
+ * Author: nek3d
+ */
+
+#include "VcfRecord.h"
+#include "SingleLineDelimTextFileReader.h"
+
+bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
+{
+ fileReader->getField(0, _chrName);
+ _chrId = fileReader->getCurrChromdId();
+ fileReader->getField(1, _startPosStr);
+ _startPos = str2chrPos(_startPosStr);
+ _startPos--; // VCF is one-based. Here we intentionally don't decrement the string version,
+ //because we'll still want to output the one-based number in the print methods, even though
+ //internally we decrement the integer to comply with the 0-based format common to other records.
+ fileReader->getField(3, _varAlt);
+ //endPos is just the startPos plus the length of the variant
+ _endPos = _startPos + _varAlt.size();
+ int2str(_endPos, _endPosStr);
+
+ fileReader->getField(2, _name);
+ fileReader->getField(4, _varRef);
+ fileReader->getField(5, _score);
+
+ return initOtherFieldsFromFile(fileReader);
+}
+
+void VcfRecord::clear()
+{
+ BedPlusInterval::clear();
+ _varAlt.clear();
+ _varRef.clear();
+}
+
+void VcfRecord::print(QuickString &outBuf) const {
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_startPosStr);
+ printOtherFields(outBuf);
+}
+
+void VcfRecord::print(QuickString &outBuf, int start, int end) const {
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_startPosStr);
+ printOtherFields(outBuf);
+}
+
+void VcfRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end) const {
+ outBuf.append(_chrName);
+ outBuf.append('\t');
+ outBuf.append(_startPosStr);
+ printOtherFields(outBuf);
+
+}
+
+void VcfRecord::printNull(QuickString &outBuf) const {
+ outBuf.append(".\t-1\t.\t.\t.\t-1");
+ for (int i= startOtherIdx; i < _numPrintFields; i++) {
+ outBuf.append("\t.");
+ }
+}
+
+void VcfRecord::printOtherFields(QuickString &outBuf) const {
+ outBuf.append('\t');
+ outBuf.append(_name);
+ outBuf.append('\t');
+ outBuf.append(_varAlt);
+ outBuf.append('\t');
+ outBuf.append(_varRef);
+ outBuf.append('\t');
+ outBuf.append(_score);
+ for (int i= 0; i < (int)_otherIdxs.size(); i++) {
+ outBuf.append('\t');
+ outBuf.append(*(_otherIdxs[i]));
+ }
+
+}
+
+const QuickString &VcfRecord::getField(int fieldNum) const
+{
+ //a request for any of the first six fields will retrieve
+ //chrom, start, end, name, score, and strand, in that order.
+ //A request for field 6+ will go to the otherIdxs.
+
+ switch (fieldNum) {
+ case 1:
+ return _chrName;
+ break;
+ case 2:
+ return _startPosStr;
+ break;
+ case 3:
+ return _name;
+ case 4:
+ return _varAlt;
+ break;
+ case 5:
+ return _varRef;
+ break;
+ case 6:
+ return _score;
+ default:
+ return BedPlusInterval::getField(fieldNum);
+ break;
+ }
+}
diff --git a/src/utils/FileRecordTools/Records/VcfRecord.h b/src/utils/FileRecordTools/Records/VcfRecord.h
new file mode 100644
index 0000000..72aafe5
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/VcfRecord.h
@@ -0,0 +1,40 @@
+/*
+ * VcfRecord.h
+ *
+ * Created on: Apr 30, 2013
+ * Author: nek3d
+ */
+
+#ifndef VCFRECORD_H_
+#define VCFRECORD_H_
+
+#include "BedPlusInterval.h"
+
+class SingleLineDelimTextFileReader;
+
+class VcfRecord : public BedPlusInterval {
+public:
+ friend class FreeList<VcfRecord>;
+
+ VcfRecord() {}
+ virtual bool initFromFile(SingleLineDelimTextFileReader *);
+ virtual void clear();
+ virtual void print(QuickString &outBuf) const;
+ virtual void print(QuickString &outBuf, int start, int end) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const;
+ virtual void printNull(QuickString &outBuf) const;
+ virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::VCF_RECORD_TYPE; }
+
+ //Note: using the assignment operator in a BedPlusInterval can potentially be a performance hit,
+ //if the number of fields frequently differ between this object and the one being copied.
+ const BedPlusInterval &operator=(const VcfRecord &other);
+
+ virtual const QuickString &getField(int fieldNum) const;
+
+protected:
+ QuickString _varAlt;
+ QuickString _varRef;
+ void printOtherFields(QuickString &outBuf) const;
+};
+
+#endif /* VCFRECORD_H_ */
diff --git a/src/utils/FileRecordTools/Records/recordsTar.tar.gz b/src/utils/FileRecordTools/Records/recordsTar.tar.gz
new file mode 100644
index 0000000..321a88e
Binary files /dev/null and b/src/utils/FileRecordTools/Records/recordsTar.tar.gz differ
diff --git a/src/utils/genomeFile/genomeFile.cpp b/src/utils/GenomeFile/GenomeFile.cpp
similarity index 98%
rename from src/utils/genomeFile/genomeFile.cpp
rename to src/utils/GenomeFile/GenomeFile.cpp
index b84948e..0f647aa 100644
--- a/src/utils/genomeFile/genomeFile.cpp
+++ b/src/utils/GenomeFile/GenomeFile.cpp
@@ -1,5 +1,5 @@
/*****************************************************************************
- genomeFile.cpp
+ GenomeFile.cpp
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -10,7 +10,7 @@
Licensed under the GNU General Public License 2.0 license.
******************************************************************************/
#include "lineFileUtilities.h"
-#include "genomeFile.h"
+#include "GenomeFile.h"
GenomeFile::GenomeFile(const string &genomeFile) {
diff --git a/src/utils/genomeFile/genomeFile.h b/src/utils/GenomeFile/GenomeFile.h
similarity index 99%
rename from src/utils/genomeFile/genomeFile.h
rename to src/utils/GenomeFile/GenomeFile.h
index a71d61e..10f6167 100644
--- a/src/utils/genomeFile/genomeFile.h
+++ b/src/utils/GenomeFile/GenomeFile.h
@@ -1,5 +1,5 @@
/*****************************************************************************
- genomeFile.h
+ GenomeFile.h
(c) 2009 - Aaron Quinlan
Hall Laboratory
diff --git a/src/utils/GenomeFile/Makefile b/src/utils/GenomeFile/Makefile
new file mode 100644
index 0000000..afaeccd
--- /dev/null
+++ b/src/utils/GenomeFile/Makefile
@@ -0,0 +1,34 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/lineFileUtilities/ \
+ -I$(UTILITIES_DIR)/BamTools/include/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= NewGenomeFile.cpp NewGenomeFile.h GenomeFile.cpp GenomeFile.h
+OBJECTS= NewGenomeFile.o GenomeFile.o
+#_EXT_OBJECTS=lineFileUtilities.o fileType.o
+#EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
+ @echo " * compiling GenomeFile.cpp"
+ @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+ @echo " * compiling NewGenomeFile.cpp"
+ @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+#$(EXT_OBJECTS):
+# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+# @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/NewGenomeFile.o $(OBJ_DIR)/GenomeFile.o
+
+.PHONY: clean
diff --git a/src/utils/GenomeFile/NewGenomeFile.cpp b/src/utils/GenomeFile/NewGenomeFile.cpp
new file mode 100644
index 0000000..d100759
--- /dev/null
+++ b/src/utils/GenomeFile/NewGenomeFile.cpp
@@ -0,0 +1,124 @@
+/*****************************************************************************
+ NewGenomeFile.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licensed under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "NewGenomeFile.h"
+#include "ParseTools.h"
+
+NewGenomeFile::NewGenomeFile(const QuickString &genomeFilename)
+: _maxId(-1)
+{
+ _genomeFileName = genomeFilename;
+ loadGenomeFileIntoMap();
+}
+
+NewGenomeFile::NewGenomeFile(const BamTools::RefVector &refVector)
+: _maxId(-1)
+{
+ for (size_t i = 0; i < refVector.size(); ++i) {
+ QuickString chrom = refVector[i].RefName;
+ CHRPOS length = refVector[i].RefLength;
+ _maxId++;
+ _chromSizeIds[chrom] = pair<CHRPOS, CHRPOS>(length, _maxId);
+ }
+}
+
+// Destructor
+NewGenomeFile::~NewGenomeFile(void) {
+}
+
+
+void NewGenomeFile::loadGenomeFileIntoMap() {
+
+
+ ifstream genFile(_genomeFileName.c_str());
+ if (!genFile.good()) {
+ cerr << "Error: Can't open genome file" << _genomeFileName << "Exiting..." << endl;
+ exit(1);
+ }
+ string sLine;
+ vector<QuickString> fields;
+ CHRPOS chrSize = 0;
+ QuickString chrName;
+ while (!genFile.eof()) {
+ sLine.clear();
+ fields.clear();
+ chrSize = 0;
+ chrName.clear();
+ getline(genFile, sLine);
+ Tokenize(sLine.c_str(), fields);
+ if (fields.size() != 2) {
+ continue;
+ }
+ chrName = fields[0];
+ chrSize = str2chrPos(fields[1]);
+ _maxId++;
+ _chromSizeIds[chrName] = pair<CHRPOS, int>(chrSize, _maxId);
+ _startOffsets.push_back(_genomeLength);
+ _genomeLength += chrSize;
+ _chromList.push_back(chrName);
+ }
+ if (_maxId == -1) {
+ cerr << "Error: The genome file " << _genomeFileName << " has no valid entries. Exiting." << endl;
+ exit(1);
+ }
+ _startOffsets.push_back(_genomeLength); //insert the final length as the last element
+ //to help with the lower_bound call in the projectOnGenome method.
+ genFile.close();
+}
+
+bool NewGenomeFile::projectOnGenome(CHRPOS genome_pos, QuickString &chrom, CHRPOS &start) {
+ // search for the chrom that the position belongs on.
+ // add 1 to genome position b/c of zero-based, half open.
+ vector<CHRPOS>::const_iterator low =
+ lower_bound(_startOffsets.begin(), _startOffsets.end(), genome_pos + 1);
+
+ // use the iterator to identify the appropriate index
+ // into the chrom name and start vectors
+ CHRPOS i = CHRPOS(low-_startOffsets.begin());
+ if (i < 0 || i >= _chromList.size()) {
+ return false; //position not on genome
+ }
+ chrom = _chromList[i - 1];
+ start = genome_pos - _startOffsets[i - 1];
+ return true;
+}
+
+CHRPOS NewGenomeFile::getChromSize(const QuickString &chrom) {
+ if (chrom == _currChromName) {
+ return _currChromSize;
+ }
+ lookupType::const_iterator iter= _chromSizeIds.find(chrom);
+ if (iter != _chromSizeIds.end()) {
+ _currChromName = iter->first;
+ _currChromSize = iter->second.first;
+ _currChromId = iter->second.second;
+ return _currChromSize;
+ }
+ cerr << "Error: chromosome " << chrom << " is not in the genome file " << _genomeFileName << ". Exiting." << endl;
+ return INT_MAX;
+}
+
+CHRPOS NewGenomeFile::getChromId(const QuickString &chrom) {
+ if (chrom == _currChromName) {
+ return _currChromId;
+ }
+ lookupType::const_iterator iter= _chromSizeIds.find(chrom);
+ if (iter != _chromSizeIds.end()) {
+ _currChromName = iter->first;
+ _currChromSize = iter->second.first;
+ _currChromId = iter->second.second;
+ return _currChromId;
+ } else {
+ cerr << "Error: requested chromosome " << chrom << " does not exist in the genome file " << _genomeFileName << ". Exiting." << endl;
+ exit(1);
+ }
+ return INT_MAX;
+}
diff --git a/src/utils/GenomeFile/NewGenomeFile.h b/src/utils/GenomeFile/NewGenomeFile.h
new file mode 100644
index 0000000..99a97fa
--- /dev/null
+++ b/src/utils/GenomeFile/NewGenomeFile.h
@@ -0,0 +1,65 @@
+
+/*****************************************************************************
+ NewGenomeFile.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licensed under the GNU General Public License 2.0 license.
+******************************************************************************/
+#ifndef NEW_GENOMEFILE_H
+#define NEW_GENOMEFILE_H
+
+#include <algorithm> // for bsearch lower_bound()
+
+#include "BedtoolsTypes.h"
+
+#include "api/BamReader.h"
+#include "api/BamAux.h"
+
+
+class NewGenomeFile {
+
+public:
+
+ NewGenomeFile(const QuickString &genomeFileName);
+ NewGenomeFile(const BamTools::RefVector &genome);
+ ~NewGenomeFile(void);
+
+ // load a GENOME file into a map keyed by chrom. value is a pair<int, int> of id and size.
+ void loadGenomeFileIntoMap();
+
+ bool projectOnGenome(CHRPOS genome_pos, QuickString &chrom, CHRPOS &start);
+
+ CHRPOS getGenomeSize(void) const { return _genomeLength; } // return the total size of the genome
+ CHRPOS getChromSize(const QuickString &chrom); // return the size of a chromosome
+ CHRPOS getChromId(const QuickString &chrom); // return chromosome's sort order
+ const vector<QuickString> &getChromList() const { return _chromList; } // return a list of chrom names
+ CHRPOS getNumberOfChroms() const { return _chromList.size(); }
+ const QuickString &getGenomeFileName() const { return _genomeFileName; }
+
+
+
+
+private:
+ QuickString _genomeFileName;
+ typedef map<QuickString, pair<CHRPOS, int> > lookupType;
+ lookupType _chromSizeIds;
+ vector<QuickString> _chromList;
+ int _maxId;
+
+ // projecting chroms onto a single coordinate system
+ CHRPOS _genomeLength;
+ vector<CHRPOS> _startOffsets;
+
+ //cache members for quick lookup
+ QuickString _currChromName;
+ CHRPOS _currChromSize;
+ int _currChromId;
+
+};
+
+#endif /* GENOMEFILE_H */
diff --git a/src/utils/NewChromsweep/Makefile b/src/utils/NewChromsweep/Makefile
new file mode 100644
index 0000000..8f4d931
--- /dev/null
+++ b/src/utils/NewChromsweep/Makefile
@@ -0,0 +1,39 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= NewChromsweep.cpp NewChromsweep.h
+OBJECTS= NewChromsweep.o
+_EXT_OBJECTS=
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/NewChromsweep.o $(BIN_DIR)/NewChromsweep.o
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
new file mode 100644
index 0000000..5e6045b
--- /dev/null
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -0,0 +1,211 @@
+/*****************************************************************************
+ NewChromsweep.cpp
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+
+#include "NewChromsweep.h"
+#include "ContextIntersect.h"
+#include "FileRecordMgr.h"
+
+NewChromSweep::NewChromSweep(ContextIntersect *context,
+ bool useMergedIntervals)
+: _context(context),
+ _queryFRM(NULL),
+ _databaseFRM(NULL),
+ _useMergedIntervals(false),
+ _queryRecordsTotalLength(0),
+ _databaseRecordsTotalLength(0),
+ _wasInitialized(false),
+ _currQueryRec(NULL),
+ _currDatabaseRec(NULL),
+ _runToQueryEnd(false)
+
+{
+}
+
+
+bool NewChromSweep::init() {
+
+ //Create new FileRecordMgrs for the two input files.
+ //Open them, and get the first record from each.
+ //if any of that goes wrong, return false;
+ //otherwise, return true.
+ _queryFRM = _context->getFile(_context->getQueryFileIdx());
+ _databaseFRM = _context->getFile(_context->getDatabaseFileIdx());
+
+ nextRecord(false);
+ if (_currDatabaseRec == NULL) {
+ return false;
+ }
+
+ //determine whether to stop when the database end is hit, or keep going until the
+ //end of the query file is hit as well.
+
+ if (_context->getNoHit() || _context->getWriteCount() || _context->getWriteOverlap() || _context->getWriteAllOverlap() || _context->getLeftJoin()) {
+ _runToQueryEnd = true;
+ }
+ _wasInitialized = true;
+ return true;
+ }
+
+void NewChromSweep::closeOut() {
+ while (!_queryFRM->eof()) {
+ nextRecord(true);
+ }
+ while (!_databaseFRM->eof()) {
+ nextRecord(false);
+ }
+}
+
+NewChromSweep::~NewChromSweep(void) {
+ if (!_wasInitialized) {
+ return;
+ }
+ _queryFRM->deleteRecord(_currQueryRec);
+ _currQueryRec = NULL;
+
+ _databaseFRM->deleteRecord(_currDatabaseRec);
+ _currDatabaseRec = NULL;
+
+ _queryFRM->close();
+ _databaseFRM->close();
+}
+
+
+void NewChromSweep::scanCache() {
+ recListIterType cacheIter = _cache.begin();
+ while (cacheIter != _cache.end())
+ {
+ const Record *cacheRec = cacheIter->value();
+ if (_currQueryRec->sameChrom(cacheRec) && !(_currQueryRec->after(cacheRec))) {
+ if (intersects(_currQueryRec, cacheRec)) {
+ _hits.push_back(cacheRec);
+ }
+ cacheIter = _cache.next();
+ }
+ else {
+ cacheIter = _cache.deleteCurrent();
+ _databaseFRM->deleteRecord(cacheRec);
+ }
+ }
+}
+
+void NewChromSweep::clearCache()
+{
+ //delete all objects pointed to by cache
+ for (recListIterType iter = _cache.begin(); iter != _cache.end(); iter = _cache.next()) {
+ _databaseFRM->deleteRecord(iter->value());
+ }
+ _cache.clear();
+}
+
+bool NewChromSweep::chromChange()
+{
+ // the files are on the same chrom
+ if (_currDatabaseRec == NULL || _currQueryRec->sameChrom(_currDatabaseRec)) {
+ return false;
+ }
+ // the query is ahead of the database. fast-forward the database to catch-up.
+ if (_currQueryRec->chromAfter(_currDatabaseRec)) {
+
+ while (_currDatabaseRec != NULL &&
+ _currQueryRec->chromAfter(_currDatabaseRec)) {
+ _databaseFRM->deleteRecord(_currDatabaseRec);
+ nextRecord(false);
+ }
+ clearCache();
+ return false;
+ }
+ // the database is ahead of the query.
+ else {
+ // 1. scan the cache for remaining hits on the query's current chrom.
+ if (_currQueryRec->getChrName() == _currChromName)
+ {
+ scanCache();
+ }
+ // 2. fast-forward until we catch up and report 0 hits until we do.
+ else if (_currQueryRec->chromBefore(_currDatabaseRec))
+ {
+ clearCache();
+ }
+
+ return true;
+ }
+}
+
+
+bool NewChromSweep::next(RecordKeyList &next) {
+ if (_currQueryRec != NULL) {
+ _queryFRM->deleteRecord(_currQueryRec);
+ }
+ nextRecord(true);
+ if (_currQueryRec == NULL) { //eof hit!
+ return false;
+ }
+
+ if (_currDatabaseRec == NULL && _cache.empty() && !_runToQueryEnd) {
+ return false;
+ }
+ _hits.clear();
+ _currChromName = _currQueryRec->getChrName();
+ // have we changed chromosomes?
+ if (!chromChange()) {
+ // scan the database cache for hits
+ scanCache();
+ //skip if we hit the end of the DB
+ // advance the db until we are ahead of the query. update hits and cache as necessary
+ while (_currDatabaseRec != NULL &&
+ _currQueryRec->sameChrom(_currDatabaseRec) &&
+ !(_currDatabaseRec->after(_currQueryRec))) {
+ if (intersects(_currQueryRec, _currDatabaseRec)) {
+ _hits.push_back(_currDatabaseRec);
+ }
+ if (_currQueryRec->after(_currDatabaseRec)) {
+ _databaseFRM->deleteRecord(_currDatabaseRec);
+ _currDatabaseRec = NULL;
+ } else {
+ _cache.push_back(_currDatabaseRec);
+ _currDatabaseRec = NULL;
+ }
+ nextRecord(false);
+ }
+ }
+ next.setKey(_currQueryRec);
+ next.setListNoCopy(_hits);
+ return true;
+}
+
+void NewChromSweep::nextRecord(bool query) {
+ if (query) {
+// if (!_context->getUseMergedIntervals()) {
+ _currQueryRec = _queryFRM->allocateAndGetNextRecord();
+// } else {
+// _currQueryRec = _queryFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
+// }
+ if (_currQueryRec != NULL) {
+ _queryRecordsTotalLength += (unsigned long)(_currQueryRec->getEndPos() - _currQueryRec->getStartPos());
+ }
+ } else { //database
+// if (!_context->getUseMergedIntervals()) {
+ _currDatabaseRec = _databaseFRM->allocateAndGetNextRecord();
+// } else {
+// _currDatabaseRec = _databaseFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
+// }
+ if (_currDatabaseRec != NULL) {
+ _databaseRecordsTotalLength += (unsigned long)(_currDatabaseRec->getEndPos() - _currDatabaseRec->getStartPos());
+ }
+ }
+}
+
+bool NewChromSweep::intersects(const Record *rec1, const Record *rec2) const
+{
+ return rec1->sameChromIntersects(rec2, _context->getSameStrand(), _context->getDiffStrand(),
+ _context->getOverlapFraction(), _context->getReciprocal());
+}
diff --git a/src/utils/NewChromsweep/NewChromsweep.h b/src/utils/NewChromsweep/NewChromsweep.h
new file mode 100644
index 0000000..9552b91
--- /dev/null
+++ b/src/utils/NewChromsweep/NewChromsweep.h
@@ -0,0 +1,96 @@
+/*****************************************************************************
+ NewChromsweepBed.h
+
+ (c) 2009 - Aaron Quinlan
+ Hall Laboratory
+ Department of Biochemistry and Molecular Genetics
+ University of Virginia
+ aaronquinlan at gmail.com
+
+ Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#ifndef NEW_CHROMSWEEP_H
+#define NEW_CHROMSWEEP_H
+
+using namespace std;
+
+#include <string>
+#include "BTlist.h"
+#include "RecordKeyList.h"
+#include <queue>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+#include "QuickString.h"
+
+class Record;
+class FileRecordMgr;
+class ContextIntersect;
+
+class NewChromSweep {
+public:
+
+ NewChromSweep(ContextIntersect *context, bool useMergedIntervals = false);
+
+
+ ~NewChromSweep(void);
+ bool init();
+
+ typedef BTlist<const Record *> recListType;
+ typedef const BTlistNode<const Record *> * recListIterType;
+ // loads next (a pair) with the current query and it's overlaps
+ bool next(RecordKeyList &next);
+
+ //MUST call this method after sweep if you want the
+ //getTotalRecordLength methods to return the whole length of the
+ //record files, rather than just what was used by sweep.
+ void closeOut();
+
+ unsigned long getQueryTotalRecordLength() { return _queryRecordsTotalLength; }
+ unsigned long getDatabaseTotalRecordLength() { return _databaseRecordsTotalLength; }
+
+ // Usage:
+ // NewChromSweep sweep = NewChromSweep(queryFileName, databaseFileName);
+ // RecordKeyList hits;
+ // while (sweep.next(hits))
+ // {
+ // processHits(hits);
+ // }
+ // getQueryTotalRecordLength()
+ // getDatabaseTotalRecordLength()
+
+private:
+ ContextIntersect *_context;
+ FileRecordMgr *_queryFRM;
+ FileRecordMgr *_databaseFRM;
+
+ bool _useMergedIntervals;
+
+ unsigned long _queryRecordsTotalLength;
+ unsigned long _databaseRecordsTotalLength;
+
+ bool _wasInitialized;
+
+ // a cache of still active features from the database file
+ recListType _cache;
+ // the set of hits in the database for the current query
+ recListType _hits;
+
+ // the current query and db features.
+ Record * _currQueryRec;
+ Record *_currDatabaseRec;
+ // a cache of the current chrom from the query. used to handle chrom changes.
+ QuickString _currChromName;
+ bool _runToQueryEnd;
+
+ void nextRecord(bool query); //true fetches next query record, false fetches next db record.
+ void nextDatabase();
+
+ void scanCache();
+ void clearCache();
+ bool chromChange();
+ bool intersects(const Record *rec1, const Record *rec2) const;
+
+};
+
+#endif /* NewChromSweep_H */
diff --git a/src/utils/RecordOutputMgr/Makefile b/src/utils/RecordOutputMgr/Makefile
new file mode 100644
index 0000000..2d196ec
--- /dev/null
+++ b/src/utils/RecordOutputMgr/Makefile
@@ -0,0 +1,39 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= RecordOutputMgr.cpp RecordOutputMgr.h
+OBJECTS= RecordOutputMgr.o
+_EXT_OBJECTS=
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/RecordOutputMgr.o
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
new file mode 100644
index 0000000..55cb70e
--- /dev/null
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -0,0 +1,430 @@
+/*
+ * RecordOutputMgr.cpp
+ *
+ * Created on: May 28, 2013
+ * Author: nek3d
+ */
+
+#include "RecordOutputMgr.h"
+#include "ContextBase.h"
+#include "ContextIntersect.h"
+#include "BlockMgr.h"
+#include "Bed3Interval.h"
+#include "Bed4Interval.h"
+#include "BedGraphInterval.h"
+#include "Bed5Interval.h"
+#include "Bed6Interval.h"
+#include "BedPlusInterval.h"
+#include "Bed12Interval.h"
+#include "BamRecord.h"
+#include "VcfRecord.h"
+#include "GffRecord.h"
+
+
+
+#include <cstdio>
+
+
+RecordOutputMgr::RecordOutputMgr()
+: _context(NULL),
+ _printable(true),
+ _bamWriter(NULL),
+ _currBamBlockList(NULL),
+ _bamBlockMgr(NULL)
+{
+ _bamBlockMgr = new BlockMgr();
+}
+
+RecordOutputMgr::~RecordOutputMgr()
+{
+ if (_outBuf.size() > 0) {
+ flush();
+ }
+ if (_bamWriter != NULL) {
+ _bamWriter->Close();
+ delete _bamWriter;
+ _bamWriter = NULL;
+ }
+ delete _bamBlockMgr;
+ _bamBlockMgr = NULL;
+
+}
+
+void RecordOutputMgr::init(ContextBase *context) {
+ _context = context;
+ if (_context->getOutputFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ //set-up BAM writer.
+ _bamWriter = new BamTools::BamWriter();
+ _bamWriter->SetCompressionMode(_context->getUncompressedBam() ? BamTools::BamWriter::Uncompressed : BamTools::BamWriter::Compressed);
+
+ int bamFileIdx = _context->getBamHeaderAndRefIdx();
+ _bamWriter->Open("stdout", _context->getFile(bamFileIdx)->getHeader().c_str(), _context->getFile(bamFileIdx)->getBamReferences());
+ } else {
+ //for everything but BAM, we'll copy output to an output buffer before printing.
+ _outBuf.reserve(MAX_OUTBUF_SIZE);
+ }
+ if (_context->getProgram() == ContextBase::INTERSECT) {
+ if ((static_cast<ContextIntersect *>(_context))->getAnyHit() || (static_cast<ContextIntersect *>(_context))->getNoHit() ||
+ (static_cast<ContextIntersect *>(_context))->getWriteCount()) {
+ _printable = false;
+ }
+ }
+}
+
+bool RecordOutputMgr::printKeyAndTerminate(RecordKeyList &keyList) {
+ printBamType bamCode = printBamRecord(keyList);
+ if (bamCode == BAM_AS_BAM) {
+ return true;
+ } else if (bamCode == NOT_BAM) {
+ keyList.getKey()->print(_outBuf);
+ return false;
+
+ }
+ //otherwise, it was BAM_AS_BED, and the key was printed.
+ return false;
+
+}
+
+RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyList &keyList, bool bamOutputOnly)
+{
+ const Record *record = keyList.getKey();
+ if (record->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ if (_context->getOutputFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ _bamWriter->SaveAlignment(static_cast<const BamRecord *>(record)->getAlignment());
+ return BAM_AS_BAM;
+ } else {
+ if (!bamOutputOnly) {
+ if (record->isUnmapped()) {
+ record->printUnmapped(_outBuf);
+ } else {
+ static_cast<const BamRecord *>(record)->print(_outBuf, _currBamBlockList);
+ }
+ }
+ return BAM_AS_BED;
+ }
+ }
+ return NOT_BAM;
+}
+
+void RecordOutputMgr::printRecord(const Record *record)
+{
+ RecordKeyList keyList(record);
+ printRecord(keyList);
+}
+
+void RecordOutputMgr::printRecord(const Record *record, const QuickString & value)
+{
+ printRecord(record);
+ _outBuf.append(value);
+ newline();
+
+ if (needsFlush()) {
+ flush();
+ }
+}
+
+void RecordOutputMgr::printRecord(RecordKeyList &keyList) {
+ if (keyList.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ RecordKeyList blockList(keyList.getKey());
+ bool deleteBlocks = false;
+ _bamBlockMgr->getBlocks(blockList, deleteBlocks);
+ printRecord(keyList, &blockList);
+ if (deleteBlocks) {
+ _bamBlockMgr->deleteBlocks(blockList);
+ }
+ return;
+ }
+ printRecord(keyList, NULL);
+
+}
+
+void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockList)
+{
+ if (needsFlush()) {
+ flush();
+ }
+ //The first time we print a record is when we print any header, because the header
+ //hasn't been read from the query file until after the first record has also been read.
+ if (_context->getPrintHeader()) {
+ checkForHeader();
+ }
+ const_cast<Record *>(keyList.getKey())->undoZeroLength();
+ _currBamBlockList = blockList;
+
+ if (_context->getProgram() == ContextBase::INTERSECT) {
+ if (_printable) {
+ if (keyList.empty()) {
+ if ((static_cast<ContextIntersect *>(_context))->getWriteAllOverlap()) {
+ // -wao the user wants to force the reporting of 0 overlap
+ if (printKeyAndTerminate(keyList)) {
+ _currBamBlockList = NULL;
+ return;
+ }
+ tab();
+ null(false, true);
+ tab();
+ _outBuf.append('0');
+ newline();
+ if (needsFlush()) flush();
+ }
+ else if ((static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
+ if (printKeyAndTerminate(keyList)) {
+ _currBamBlockList = NULL;
+ return;
+ }
+ tab();
+ null(false, true);
+ newline();
+ if (needsFlush()) flush();
+ _currBamBlockList = NULL;
+ return;
+ }
+ } else {
+ if (printBamRecord(keyList, true) == BAM_AS_BAM) {
+ _currBamBlockList = NULL;
+ return;
+ }
+ int hitIdx = 0;
+ for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ reportOverlapDetail(keyList.getKey(), iter->value(), hitIdx);
+ hitIdx++;
+ }
+ }
+ } else { // not printable
+ reportOverlapSummary(keyList);
+ }
+ _currBamBlockList = NULL;
+ } else if (_context->getProgram() == ContextBase::SAMPLE) {
+ if (!printKeyAndTerminate(keyList)) {
+ newline();
+ }
+ _currBamBlockList = NULL;
+ return;
+ } else if (_context->getProgram() == ContextBase::MAP) {
+ if (!printKeyAndTerminate(keyList)) {
+ tab();
+ }
+ _currBamBlockList = NULL;
+ return;
+ }
+}
+
+void RecordOutputMgr::checkForHeader() {
+ //if the program is based on intersection, we want the header from the query file.
+ if (_context->hasIntersectMethods()) {
+ int queryIdx = (static_cast<ContextIntersect *>(_context))->getQueryFileIdx();
+ const QuickString &header = _context->getFile(queryIdx)->getHeader();
+ _outBuf.append(header);
+ } else {
+ _outBuf.append(_context->getFile(0)->getHeader());
+ }
+ _context->setPrintHeader(false);
+ if (needsFlush()) flush();
+}
+
+void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx)
+{
+ //get the max start and min end as strings.
+ const_cast<Record *>(hitRecord)->undoZeroLength();
+
+
+ const QuickString *startStr = NULL;
+ const QuickString *endStr = NULL;
+ int maxStart = 0;
+ int minEnd = 0;
+
+ int keyStart = keyRecord->getStartPos();
+ int keyEnd = keyRecord->getEndPos();
+ int hitStart = hitRecord->getStartPos();
+ int hitEnd = hitRecord->getEndPos();
+
+ if ( keyStart>= hitStart) {
+ //the key start is after the hit start, but we need to check and make sure the hit end is at least after the keyStart.
+ //The reason for this is that, in some rare cases, such as both the key and hit having been zero length intervals,
+ //the normal process for intersection that allows us to simply report the maxStart and minEnd do not necessarily apply.
+ if (hitEnd >= keyStart) {
+ //this is ok. We have a normal intersection where the key comes after the hit.
+
+ maxStart = keyStart;
+ startStr = &(keyRecord->getStartPosStr());
+
+ minEnd = min(keyEnd, hitEnd);
+ endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
+
+ } else {
+ //this is the weird case of not a "real" intersection. The keyStart is greater than the hitEnd. So just report the key as is.
+ maxStart = keyStart;
+ minEnd = keyEnd;
+ startStr = &(keyRecord->getStartPosStr());
+ endStr = &(keyRecord->getEndPosStr());
+ }
+
+ } else {
+ //all of the above, but backwards. keyStart is before hitStart.
+ if (keyEnd >= hitStart) {
+ //normal intersection, key first
+ maxStart = hitStart;
+ startStr = &(hitRecord->getStartPosStr());
+ minEnd = min(keyEnd, hitEnd);
+ endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
+ } else {
+ //this is the weird case of not a "real" intersection. The hitStart is greater than the keyEnd. So just report the hit as is.
+ maxStart = hitStart;
+ minEnd = hitEnd;
+ startStr = &(hitRecord->getStartPosStr());
+ endStr = &(hitRecord->getEndPosStr());
+
+ }
+ }
+
+
+ if (!(static_cast<ContextIntersect *>(_context))->getWriteA() && !(static_cast<ContextIntersect *>(_context))->getWriteB()
+ && !(static_cast<ContextIntersect *>(_context))->getWriteOverlap() && !(static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
+ printKey(keyRecord, *startStr, *endStr);
+ newline();
+ if (needsFlush()) flush();
+ }
+ else if (((static_cast<ContextIntersect *>(_context))->getWriteA() &&
+ (static_cast<ContextIntersect *>(_context))->getWriteB()) || (static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
+ printKey(keyRecord);
+ tab();
+ hitRecord->print(_outBuf);
+ newline();
+ if (needsFlush()) flush();
+ }
+ else if ((static_cast<ContextIntersect *>(_context))->getWriteA()) {
+ printKey(keyRecord);
+ newline();
+ if (needsFlush()) flush();
+ }
+ else if ((static_cast<ContextIntersect *>(_context))->getWriteB()) {
+ printKey(keyRecord, *startStr, *endStr);
+ tab();
+ hitRecord->print(_outBuf);
+ newline();
+ if (needsFlush()) flush();
+ }
+ else if ((static_cast<ContextIntersect *>(_context))->getWriteOverlap()) {
+ int printOverlapBases = 0;
+ if (_context->getObeySplits()) {
+ printOverlapBases = _splitInfo->getOverlapBases(hitIdx);
+ } else {
+ printOverlapBases = minEnd - maxStart;
+ }
+ printKey(keyRecord);
+ tab();
+ hitRecord->print(_outBuf);
+ tab();
+ int2str(printOverlapBases, _outBuf, true);
+ newline();
+ if (needsFlush()) flush();
+ }
+}
+
+void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
+{
+ int numOverlapsFound = (int)keyList.size();
+ if ((static_cast<ContextIntersect *>(_context))->getAnyHit() && numOverlapsFound > 0) {
+ if (printKeyAndTerminate(keyList)) {
+ return;
+ }
+ newline();
+ if (needsFlush()) flush();
+ } else if ((static_cast<ContextIntersect *>(_context))->getWriteCount()) {
+ if (printKeyAndTerminate(keyList)) {
+ return;
+ }
+ tab();
+ int2str(numOverlapsFound, _outBuf, true);
+ newline();
+ if (needsFlush()) flush();
+ } else if ((static_cast<ContextIntersect *>(_context))->getNoHit() && numOverlapsFound == 0) {
+ if (printKeyAndTerminate(keyList)) {
+ return;
+ }
+ newline();
+ if (needsFlush()) flush();
+ }
+}
+
+
+void RecordOutputMgr::null(bool queryType, bool dbType)
+{
+ FileRecordTypeChecker::RECORD_TYPE recordType = FileRecordTypeChecker::UNKNOWN_RECORD_TYPE;
+ if (_context->hasIntersectMethods()) {
+ if (queryType) {
+ recordType = (static_cast<ContextIntersect *>(_context))->getQueryRecordType();
+ } else if (dbType) {
+ recordType = (static_cast<ContextIntersect *>(_context))->getDatabaseRecordType();
+ }
+ } else {
+ recordType = _context->getFile(0)->getRecordType();
+ }
+ //This is kind of a hack. Need an instance of the correct class of record in order to call it's printNull method.
+ Record *dummyRecord = NULL;
+
+ switch (recordType) {
+ case FileRecordTypeChecker::BED3_RECORD_TYPE:
+ dummyRecord = new Bed3Interval();
+ break;
+ case FileRecordTypeChecker::BED4_RECORD_TYPE:
+ dummyRecord = new Bed4Interval();
+ break;
+ case FileRecordTypeChecker::BEDGRAPH_RECORD_TYPE:
+ dummyRecord = new BedGraphInterval();
+ break;
+ case FileRecordTypeChecker::BED5_RECORD_TYPE:
+ dummyRecord = new Bed5Interval();
+ break;
+ case FileRecordTypeChecker::BED6_RECORD_TYPE:
+ dummyRecord = new Bed6Interval();
+ break;
+ case FileRecordTypeChecker::BED12_RECORD_TYPE:
+ dummyRecord = new Bed12Interval();
+ break;
+ case FileRecordTypeChecker::BED_PLUS_RECORD_TYPE:
+ dummyRecord = new BedPlusInterval();
+ (static_cast<BedPlusInterval *>(dummyRecord))->setNumPrintFields((static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields());
+ break;
+ case FileRecordTypeChecker::VCF_RECORD_TYPE:
+ dummyRecord = new VcfRecord();
+ (static_cast<VcfRecord *>(dummyRecord))->setNumPrintFields((static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields());
+ break;
+ case FileRecordTypeChecker::BAM_RECORD_TYPE:
+ dummyRecord = new BamRecord();
+ break;
+ case FileRecordTypeChecker::GFF_RECORD_TYPE:
+ dummyRecord = new GffRecord();
+ (static_cast<GffRecord *>(dummyRecord))->setNumFields((static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields());
+ break;
+ default:
+ break;
+ }
+
+ dummyRecord->printNull(_outBuf);
+ delete dummyRecord;
+
+}
+
+void RecordOutputMgr::printKey(const Record *key, const QuickString & start, const QuickString & end)
+{
+ if (key->getType() != FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ key->print(_outBuf, start, end);
+ } else {
+ static_cast<const BamRecord *>(key)->print(_outBuf, start, end, _currBamBlockList);
+ }
+}
+
+void RecordOutputMgr::printKey(const Record *key)
+{
+ if (key->getType() != FileRecordTypeChecker::BAM_RECORD_TYPE) {
+ key->print(_outBuf);
+ } else {
+ static_cast<const BamRecord *>(key)->print(_outBuf, _currBamBlockList);
+ }
+}
+
+void RecordOutputMgr::flush() {
+ fwrite(_outBuf.c_str(), 1, _outBuf.size(), stdout);
+ _outBuf.clear();
+}
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.h b/src/utils/RecordOutputMgr/RecordOutputMgr.h
new file mode 100644
index 0000000..b6296fd
--- /dev/null
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.h
@@ -0,0 +1,72 @@
+/*
+ * RecordOutputMgr.h
+ *
+ * Created on: May 28, 2013
+ * Author: nek3d
+ */
+
+#ifndef RECORDOUTPUTMGR_H_
+#define RECORDOUTPUTMGR_H_
+
+using namespace std;
+
+#include "ContextBase.h"
+#include "RecordKeyList.h"
+#include "api/BamWriter.h"
+
+class BlockMgr;
+
+class RecordOutputMgr {
+public:
+ RecordOutputMgr();
+ ~RecordOutputMgr();
+
+ //The init method must be called after all the input files are open.
+ void init(ContextBase *context);
+
+ void printRecord(const Record *record);
+ void printRecord(RecordKeyList &keyList);
+ void printRecord(const Record *record, const QuickString & value);
+
+ //where necessary, pass additional information about splits through the blockMgr.
+ void setSplitInfo(const BlockMgr *blockMgr) { _splitInfo = blockMgr; }
+
+private:
+ typedef enum { NOT_BAM, BAM_AS_BAM, BAM_AS_BED} printBamType;
+
+ ContextBase *_context;
+ bool _printable;
+ BamTools::BamWriter *_bamWriter;
+ RecordKeyList *_currBamBlockList;
+
+ QuickString _outBuf;
+
+ //
+ BlockMgr *_bamBlockMgr;
+ const BlockMgr *_splitInfo;
+ //some helper functions to neaten the code.
+ void tab() { _outBuf.append('\t'); }
+ void newline() { _outBuf.append('\n'); }
+ void null(bool queryType, bool dbType);
+
+ void printRecord(RecordKeyList &keyList, RecordKeyList *blockList);
+ void printKey(const Record *key);
+ void printKey(const Record *key, const QuickString & start, const QuickString & end);
+ bool printKeyAndTerminate(RecordKeyList &keyList);
+ printBamType printBamRecord(RecordKeyList &keyList, bool bamOutputOnly = false);
+ void checkForHeader();
+ void reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx = 0);
+ void reportOverlapSummary(RecordKeyList &keyList);
+
+ static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
+
+ // If we are using buffered output, only flush the output buffer if it's least
+ // 90% full. If we're not using buffered output, flush if it's not empty
+ bool needsFlush() const {
+ return ((_context->getUseBufferedOutput() &&_outBuf.size() >= MAX_OUTBUF_SIZE *.9) ||
+ (!_context->getUseBufferedOutput() && !_outBuf.empty()));
+ }
+ void flush();
+};
+
+#endif /* RECORDOUTPUTMGR_H_ */
diff --git a/src/utils/VectorOps/VectorOps.cpp b/src/utils/VectorOps/VectorOps.cpp
index 53c2c37..7416f44 100644
--- a/src/utils/VectorOps/VectorOps.cpp
+++ b/src/utils/VectorOps/VectorOps.cpp
@@ -25,6 +25,17 @@ double MakeDouble(const string &element) {
return x;
}
+// functor to convert the abs() of single string to a double
+double MakeAbsDouble(const string &element) {
+ std::istringstream i(element);
+ double x;
+ if (!(i >> x)) {
+ cerr << "Error: Could not properly convert string to numeric (\"" + element + "\")" << endl;
+ exit(1);
+ }
+ return fabs(x);
+}
+
struct ValueGreaterThan
{
bool operator()( const vector< pair<int, string> >::value_type& lhs,
@@ -127,6 +138,13 @@ double VectorOps::GetMin(void)
return *min_element( _vecd.begin(), _vecd.end() );
}
+double VectorOps::GetAbsMin(void)
+{
+ // convert the vec of strings to a vec of doubles
+ transform(_vecs.begin(), _vecs.end(), back_inserter(_vecd), MakeAbsDouble);
+ return *min_element( _vecd.begin(), _vecd.end() );
+}
+
double VectorOps::GetMax(void)
{
// convert the vec of strings to a vec of doubles
@@ -134,6 +152,12 @@ double VectorOps::GetMax(void)
return *max_element( _vecd.begin(), _vecd.end() );
}
+double VectorOps::GetAbsMax(void)
+{
+ // convert the vec of strings to a vec of doubles
+ transform(_vecs.begin(), _vecs.end(), back_inserter(_vecd), MakeAbsDouble);
+ return *max_element( _vecd.begin(), _vecd.end() );
+}
string VectorOps::GetMode(void)
{
@@ -208,12 +232,12 @@ uint32_t VectorOps::GetCountDistinct(void)
return _vecs.size();
}
-string VectorOps::GetCollapse(void)
+string VectorOps::GetCollapse(string delimiter)
{
ostringstream collapse;
for( size_t i = 0; i < _vecs.size(); i++ ) {
if (i>0)
- collapse << ",";
+ collapse << delimiter;
collapse << _vecs[i];
}
return collapse.str();
diff --git a/src/utils/VectorOps/VectorOps.h b/src/utils/VectorOps/VectorOps.h
index 3f4b53c..90d45a8 100644
--- a/src/utils/VectorOps/VectorOps.h
+++ b/src/utils/VectorOps/VectorOps.h
@@ -59,12 +59,16 @@ public:
double GetMin(void);
// return the maximum element of the vector
double GetMax(void);
+ // return the minimum absolute value of the vector
+ double GetAbsMin(void);
+ // return the maximum absolute value of the vector
+ double GetAbsMax(void);
// return the count of element in the vector
uint32_t GetCount(void);
// return a the count of _unique_ elements in the vector
uint32_t GetCountDistinct(void);
- // return a comma-separated list of elements
- string GetCollapse(void);
+ // return a delimiter-separated list of elements
+ string GetCollapse(string delimiter = ",");
// return a concatenation of all elements in the vector
string GetConcat(void);
// return a comma-separated list of the _unique_ elements
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 4b8022f..ea993af 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -79,7 +79,20 @@ BedFile::BedFile(string &bedFile)
_merged_end(-1),
_merged_chrom(""),
_prev_start(-1),
- _prev_chrom("")
+ _prev_chrom(""),
+ _total_length(0)
+{}
+
+BedFile::BedFile(void)
+: _isGff(false),
+ _isVcf(false),
+ _typeIsKnown(false),
+ _merged_start(-1),
+ _merged_end(-1),
+ _merged_chrom(""),
+ _prev_start(-1),
+ _prev_chrom(""),
+ _total_length(0)
{}
// Destructor
@@ -101,10 +114,14 @@ void BedFile::Open(void) {
delete _bedStream;
_bedStream = new igzstream(bedFile.c_str(), ios::in);
}
- if ( !(_bedStream->good()) ) {
- cerr << "Error: The requested bed file ("
- << bedFile
- << ") could not be opened. Exiting!" << endl;
+ if ( _bedStream->fail() ) {
+ cerr << "Error: The requested file ("
+ << bedFile
+ << ") "
+ << "could not be opened. "
+ << "Error message: ("
+ << strerror(errno)
+ << "). Exiting!" << endl;
exit (1);
}
}
@@ -139,6 +156,11 @@ void BedFile::Close(void) {
void BedFile::GetLine(void) {
// parse the bedStream pointer
getline(*_bedStream, _bedLine);
+
+ // ditch \r for Windows.
+ if (_bedLine[_bedLine.size()-1] == '\r') {
+ _bedLine.resize(_bedLine.size()-1);
+ }
// increment the line number
_lineNum++;
// split into a string vector.
@@ -196,6 +218,11 @@ bool BedFile::GetNextBed(BED &bed, bool forceSorted) {
else {
// handle the first line as a special case because
// of reading the header.
+
+ // ditch \r for Windows if necessary.
+ if (_bedLine[_bedLine.size()-1] == '\r') {
+ _bedLine.resize(_bedLine.size()-1);
+ }
Tokenize(_bedLine, _bedFields);
_firstLine = false;
setBedType(_bedFields.size());
@@ -225,6 +252,7 @@ bool BedFile::GetNextBed(BED &bed, bool forceSorted) {
_prev_chrom = bed.chrom;
_prev_start = bed.start;
}
+ _total_length += (bed.end - bed.start);
return true;
}
else if (_status == BED_HEADER || _status == BED_BLANK)
@@ -259,6 +287,8 @@ bool BedFile::GetNextMergedBed(BED &merged_bed) {
_merged_start = bed.start;
_merged_end = bed.end;
+ _total_flattened_length += \
+ (merged_bed.end - merged_bed.start);
return true;
}
else {
@@ -281,6 +311,9 @@ bool BedFile::GetNextMergedBed(BED &merged_bed) {
merged_bed.chrom = _merged_chrom;
merged_bed.start = _merged_start;
merged_bed.end = _merged_end;
+
+ _total_flattened_length += \
+ (merged_bed.end - merged_bed.start);
return true;
}
}
@@ -289,6 +322,14 @@ bool BedFile::GetNextMergedBed(BED &merged_bed) {
}
+unsigned long BedFile::getTotalLength(void) {
+ return _total_length;
+}
+
+unsigned long BedFile::getTotalFlattenedLength(void) {
+ return _total_flattened_length;
+}
+
void BedFile::allHits(string chrom, CHRPOS start,
CHRPOS end, string strand,
vector<BED> &hits, bool sameStrand,
@@ -627,6 +668,11 @@ void BedFile::loadBedFileIntoMap() {
Close();
}
+void BedFile::addBEDIntoMap(BED bedEntry) {
+ BIN bin = getBin(bedEntry.start, bedEntry.end);
+ bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+}
+
void BedFile::loadBedCovFileIntoMap() {
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 3158103..37d8dda 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -380,6 +380,7 @@ public:
// Constructor
BedFile(string &);
+ BedFile(void);
// Destructor
~BedFile(void);
@@ -418,6 +419,9 @@ public:
// vector of BEDs
void loadBedFileIntoMap();
+ // load a BED entry into and existing map
+ void addBEDIntoMap(BED bedEntry);
+
// load a BED file into a map keyed by chrom, then bin. value is
// vector of BEDCOVs
void loadBedCovFileIntoMap();
@@ -461,6 +465,16 @@ public:
// that the feature overlaps
void countListHits(const BED &a, int index,
bool sameStrand, bool diffStrand);
+
+
+ // return the total length of all the intervals in the file.
+ // use with GetNextBed()
+ unsigned long getTotalLength(void);
+
+ // return the total _flattened_ length of all the intervals in the file.
+ // use with GetNextMergedBed()
+ unsigned long getTotalFlattenedLength(void);
+
// the bedfile with which this instance is associated
string bedFile;
@@ -498,6 +512,8 @@ private:
string _merged_chrom;
int _prev_start;
string _prev_chrom;
+ unsigned long _total_length;
+ unsigned long _total_flattened_length;
void setZeroBased(bool zeroBased);
void setGff (bool isGff);
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index 31e6178..2c2122c 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -36,8 +36,14 @@ void BedFilePE::Open(void) {
_bedStream = new igzstream(bedFile.c_str(), ios::in);
}
// can we open the file?
- if ( !(_bedStream->good()) ) {
- cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
+ if ( _bedStream->fail() ) {
+ cerr << "Error: The requested BEDPE file ("
+ << bedFile
+ << ") "
+ << "could not be opened. "
+ << "Error message: ("
+ << strerror(errno)
+ << "). Exiting!" << endl;
exit (1);
}
}
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index 1967a9c..b9f5157 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -38,8 +38,14 @@ void BedGraphFile::Open() {
_bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
}
// can we open the file?
- if ( !(_bedGraphStream->good()) ) {
- cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
+ if ( _bedGraphStream->fail() ) {
+ cerr << "Error: The requested file ("
+ << bedGraphFile
+ << ") "
+ << "could not be opened. "
+ << "Error message: ("
+ << strerror(errno)
+ << "). Exiting!" << endl;
exit (1);
}
}
diff --git a/src/utils/bedGraphFile/bedGraphFile.h b/src/utils/bedGraphFile/bedGraphFile.h
index 41e860d..dcbb6a6 100644
--- a/src/utils/bedGraphFile/bedGraphFile.h
+++ b/src/utils/bedGraphFile/bedGraphFile.h
@@ -139,6 +139,9 @@ public:
// split into a string vector.
Tokenize(bedGraphLine,bedGraphFields);
+ if (bedGraphLine[bedGraphLine.size()-1] == '\r') {
+ bedGraphLine.resize(bedGraphLine.size()-1);
+ }
// load the BED struct as long as it's a valid BED entry.
return parseLine(bedgraph, bedGraphFields, lineNum);
diff --git a/src/utils/chromsweep/chromsweep.cpp b/src/utils/chromsweep/chromsweep.cpp
index 4c800fa..d9b864c 100644
--- a/src/utils/chromsweep/chromsweep.cpp
+++ b/src/utils/chromsweep/chromsweep.cpp
@@ -144,7 +144,7 @@ bool ChromSweep::IsValidHit(const BED &query, const BED &db) {
int overlapBases = (e - s);
// 1. is there sufficient overlap w.r.t A?
if ( (float) overlapBases / (float) aLength >= _overlapFraction) {
- CHRPOS bLength = (db.end - query.start);
+ CHRPOS bLength = (db.end - db.start);
float bOverlap = ( (float) overlapBases / (float) bLength );
// Now test for necessary strandedness.
diff --git a/src/utils/fileType/FileRecordTypeChecker.cpp b/src/utils/fileType/FileRecordTypeChecker.cpp
new file mode 100644
index 0000000..370cfff
--- /dev/null
+++ b/src/utils/fileType/FileRecordTypeChecker.cpp
@@ -0,0 +1,387 @@
+
+#include "FileRecordTypeChecker.h"
+#include "api/BamReader.h"
+#include "ParseTools.h"
+
+FileRecordTypeChecker::FileRecordTypeChecker()
+{
+ _fileType = UNKNOWN_FILE_TYPE;
+ _recordType = UNKNOWN_RECORD_TYPE;
+ _numFields = 0;
+ _isBinary = false;
+ _isText = false;
+ _isBed = false;
+ _isDelimited = false;
+ _delimChar = '\0';
+ _lines.clear();
+ _firstValidDataLineIdx = -1;
+ _isVCF = false;
+ _isBAM = false;
+ _isGFF = false;
+ _isGzipped = false;
+ _insufficientData = false;
+ _fourthFieldNumeric = false;
+
+ _hasName[UNKNOWN_RECORD_TYPE] = false;
+ _hasName[BED3_RECORD_TYPE] = false;
+ _hasName[BED6_RECORD_TYPE] = true;
+ _hasName[BED12_RECORD_TYPE] = true;
+ _hasName[BED_PLUS_RECORD_TYPE] = true;
+ _hasName[BAM_RECORD_TYPE] = true;
+ _hasName[VCF_RECORD_TYPE] = true;
+ _hasName[GFF_RECORD_TYPE] = true;
+
+ _hasScore[UNKNOWN_RECORD_TYPE] = false;
+ _hasScore[BED3_RECORD_TYPE] = false;
+ _hasScore[BED6_RECORD_TYPE] = true;
+ _hasScore[BED12_RECORD_TYPE] = true;
+ _hasScore[BED_PLUS_RECORD_TYPE] = true;
+ _hasScore[BAM_RECORD_TYPE] = true;
+ _hasScore[VCF_RECORD_TYPE] = true;
+ _hasScore[GFF_RECORD_TYPE] = true;
+
+ _hasStrand[UNKNOWN_RECORD_TYPE] = false;
+ _hasStrand[BED3_RECORD_TYPE] = false;
+ _hasStrand[BED6_RECORD_TYPE] = true;
+ _hasStrand[BED12_RECORD_TYPE] = true;
+ _hasStrand[BED_PLUS_RECORD_TYPE] = true;
+ _hasStrand[BAM_RECORD_TYPE] = true;
+ _hasStrand[VCF_RECORD_TYPE] = true;
+ _hasStrand[GFF_RECORD_TYPE] = true;
+
+ _recordTypeNames[UNKNOWN_RECORD_TYPE] = "Unknown record type";
+ _recordTypeNames[BED3_RECORD_TYPE] = "Bed3 record type";
+ _recordTypeNames[BED6_RECORD_TYPE] = "Bed6 record type";
+ _recordTypeNames[BED12_RECORD_TYPE] = "Bed12 record type";
+ _recordTypeNames[BED_PLUS_RECORD_TYPE] = "BedPlus record type";
+ _recordTypeNames[BAM_RECORD_TYPE] = "BAM record type";
+ _recordTypeNames[VCF_RECORD_TYPE] = "VCF record type";
+ _recordTypeNames[GFF_RECORD_TYPE] = "GFF record type";
+
+// UNKNOWN_FILE_TYPE, SINGLE_LINE_DELIM_TEXT_FILE_TYPE,
+// MULTI_LINE_ENTRY_TEXT_FILE_TYPE,
+// GFF_FILE_TYPE, GZIP_FILE_TYPE, BAM_FILE_TYPE
+
+ _fileTypeNames[UNKNOWN_FILE_TYPE] = "Unknown file type";
+ _fileTypeNames[SINGLE_LINE_DELIM_TEXT_FILE_TYPE] = "Delimited text file type";
+ _fileTypeNames[GZIP_FILE_TYPE] = "Gzip file type";
+ _fileTypeNames[BAM_FILE_TYPE] = "BAM file type";
+ _fileTypeNames[VCF_FILE_TYPE] = "VCF file type";
+}
+
+
+bool FileRecordTypeChecker::scanBuffer(const char *buffer, size_t len)
+{
+ if (len == 0) {
+ len = strlen(buffer);
+ }
+ _numBytesInBuffer = len;
+ if (_numBytesInBuffer == 0) {
+ cerr << "Error: " << _filename << " is an empty file."<< endl;
+ exit(1);
+ }
+
+ //special: the first thing we do is look for a gzipped file.
+ if (!_isGzipped && ((unsigned char)(buffer[0]) == 0x1f)) {
+ _isGzipped = true;
+ return true;
+ }
+ //scan the first 8K block of the streamBuf.
+
+ //now we have a buffer from the file.
+ //first, test to see if it's binary or text.
+ if (isBinaryBuffer(buffer, len)) {
+ _isText = false;
+ _isBinary = true;
+ return true;
+ } else {
+ _isText = true;
+ _isBinary = false;
+ return handleTextFormat(buffer, len);
+ }
+}
+
+bool FileRecordTypeChecker::isBinaryBuffer(const char *buffer, size_t len)
+{
+ if (isBAM(buffer)) {
+ return true;
+ }
+
+ //Let's say that in a text file, at least 90% of the characters
+ //should be alphanumeric, whitespace, or punctuation.
+
+ int alphaNumCount = 0;
+ int whiteSpaceCount = 0;
+ int punctuationCount = 0;
+
+ for (int i=0; i < (int)len; i++) {
+ char currChar = buffer[i];
+ if (isalnum(currChar)) {
+ alphaNumCount++;
+ } else if (isspace(currChar)) {
+ whiteSpaceCount++;
+ } else if (ispunct(currChar)) {
+ punctuationCount++;
+ }
+ }
+
+ if ((float)(alphaNumCount + whiteSpaceCount + punctuationCount) / (float)(_numBytesInBuffer) < PERCENTAGE_PRINTABLE) {
+ return true;
+ }
+ return false;
+}
+
+
+bool FileRecordTypeChecker::isBAM(const char *buffer)
+{
+ //check for BAM. The Bam Magic String is "BAM\1", and should be the first 4 characters of the file.
+
+ if (strncmp(buffer, "BAM\1", 4) == 0) {
+ _isBAM = true;
+ _fileType = BAM_FILE_TYPE;
+ _recordType = BAM_RECORD_TYPE;
+ return true;
+ }
+
+ //TBD: Handle other binary formats
+ return false;
+}
+
+bool FileRecordTypeChecker::handleTextFormat(const char *buffer, size_t len)
+{
+ if (isVCFformat(buffer)) {
+ return isTextDelimtedFormat(buffer, len);
+ } else if (isTextDelimtedFormat(buffer, len)) {
+
+ //At this point, _isText and _isDelimited are set. _numFields and _delimChar are
+ //set.
+ _fileType = SINGLE_LINE_DELIM_TEXT_FILE_TYPE;
+
+ //Tokenize the first line of valid data into fields.
+ const QuickString &line = _lines[_firstValidDataLineIdx];
+ _currLineElems.clear();
+ if (Tokenize(line, _currLineElems, _delimChar, _numFields) != _numFields) {
+ cerr << "Error: Type checker found wrong number of fields while tokenizing data line." << endl;
+ exit(1);
+ }
+
+ if (isBedFormat()) {
+ _isBed = true;
+ if (_numFields == 3) {
+ _recordType = BED3_RECORD_TYPE;
+ } else if (_numFields == 4) {
+ if (isNumeric(_currLineElems[3])) {
+ _recordType = BEDGRAPH_RECORD_TYPE;
+ _fourthFieldNumeric = true;
+ } else {
+ _fourthFieldNumeric = false;
+ _recordType = BED4_RECORD_TYPE;
+ }
+ } else if (_numFields == 5) {
+ _recordType = BED5_RECORD_TYPE;
+ } else if (_numFields == 6) {
+ _recordType = BED6_RECORD_TYPE;
+ } else if (_numFields == 12) {
+ _recordType = BED12_RECORD_TYPE;
+ } else if (_numFields >6) {
+ _recordType = BED_PLUS_RECORD_TYPE;
+ }
+ return true;
+ }
+ if (isGFFformat()) {
+ _isGFF = true;
+ _recordType = GFF_RECORD_TYPE;
+ return true;
+ }
+ return false;
+ }
+ return false;
+}
+
+bool FileRecordTypeChecker::isVCFformat(const char *buffer)
+{
+ if (_isVCF) {
+ return true; //previous pass through this method has determined file is VCF.
+ }
+ if (memcmp(buffer, "##fileformat=VCF", 16) == 0) {
+ _isVCF = true;
+ _fileType = VCF_FILE_TYPE;
+ _recordType = VCF_RECORD_TYPE;
+ return true;
+ }
+ return false;
+}
+
+bool FileRecordTypeChecker::isBedFormat() {
+
+ //test that the file has at least three fields.
+ //2nd and 3rd fields of first valid data line must be integers. 3rd must not be less than 2nd.
+ if (_numFields < 3) {
+ return false;
+ }
+ //the 2nd and 3rd fields must be numeric.
+ if (!isNumeric(_currLineElems[1]) || !isNumeric(_currLineElems[2])) {
+ return false;
+ }
+
+ int start = str2chrPos(_currLineElems[1]);
+ int end = str2chrPos(_currLineElems[2]);
+ if (end < start) {
+ return false;
+ }
+ return true;
+}
+
+bool FileRecordTypeChecker::isGFFformat()
+{
+ //a GFF file may have 8 or 9 fields.
+ if (_numFields < 7 || _numFields > 9) {
+ return false;
+ }
+ //the 4th and 5th fields must be numeric.
+ if (!isNumeric(_currLineElems[3]) || !isNumeric(_currLineElems[4])) {
+ return false;
+ }
+ int start = str2chrPos(_currLineElems[3]);
+ int end = str2chrPos(_currLineElems[4]);
+ if (end < start) {
+ return false;
+ }
+ return true;
+}
+
+bool FileRecordTypeChecker::isTextDelimtedFormat(const char *buffer, size_t len)
+{
+ //Break single string buffer into vector of QuickStrings. Delimiter is newline.
+ _lines.clear();
+ int numLines = Tokenize(buffer, _lines, '\n', len);
+
+ //anticipated delimiter characters are tab, comma, and semi-colon.
+ //If we need new ones, they must be added in this method.
+ //search each line for delimiter characters.
+
+ vector<int> tabCounts;
+ vector<int> commaCounts;
+ vector<int> semicolonCounts;
+
+ tabCounts.reserve(numLines);
+ commaCounts.reserve(numLines);
+ semicolonCounts.reserve(numLines);
+
+ //loop through the lines, ignoring headers. Count potential delimiters,
+ //see if we can find a few lines with the same number of a given delimiter.
+ //delims are tested in hierarchical order, starting with tab,then comma, then semi-colon.
+
+ int validLinesFound=0;
+ int headerCount = 0;
+ int emptyLines = 0;
+ for (int i=0; i < numLines; i++ ) {
+
+ if (validLinesFound >=4) {
+ break; //really only need to look at like 4 lines of data, max.
+ }
+ QuickString &line = _lines[i];
+ int len =line.size();
+ //skip over any empty line
+ if (len == 0) {
+ emptyLines++;
+ continue;
+ }
+
+ //skip over any header line
+ if (isHeaderLine(line)) {
+ //clear any previously found supposedly valid data lines, because valid lines can only come after header lines.
+ if (_firstValidDataLineIdx > -1 && _firstValidDataLineIdx < i) {
+ _firstValidDataLineIdx = -1;
+ validLinesFound--;
+ headerCount++;
+ }
+ headerCount++;
+ continue;
+ }
+ //a line must have some alphanumeric characters in order to be valid.
+ bool hasAlphaNum = false;
+ for (int j=0; j < len; j++) {
+ if(isalnum(line[j])) {
+ hasAlphaNum = true;
+ break;
+ }
+ }
+ if (!hasAlphaNum) {
+ continue;
+ }
+
+ validLinesFound++;
+ if (_firstValidDataLineIdx == -1) {
+ _firstValidDataLineIdx = i;
+ }
+
+ int lineTabCount = 0, lineCommaCount=0, lineSemicolonCount =0;
+ for (int j=0; j < len; j++) {
+ char currChar = line[j];
+ if (currChar == '\t') {
+ lineTabCount++;
+ } else if (currChar == ',') {
+ lineCommaCount++;
+ } else if (currChar == ';') {
+ lineSemicolonCount++;
+ }
+ }
+ tabCounts.push_back(lineTabCount);
+ commaCounts.push_back(lineCommaCount);
+ semicolonCounts.push_back(lineSemicolonCount);
+ }
+
+ if (headerCount + emptyLines == numLines) {
+ _insufficientData = true;
+ }
+ if (validLinesFound == 0) {
+ return false;
+ }
+ _insufficientData = false;
+
+ if (delimiterTesting(tabCounts, '\t')) {
+ return true;
+ }
+ if (delimiterTesting(commaCounts, ',')) {
+ return true;
+ }
+ if (delimiterTesting(semicolonCounts, ';')) {
+ return true;
+ }
+
+ return false; //unable to detect delimited file.
+}
+
+bool FileRecordTypeChecker::delimiterTesting(vector<int> &counts, char suspectChar)
+{
+ //check to see if we found the same number of tabs in every line.
+ int numDelims = counts[0];
+ if (numDelims != 0) {
+ bool countsMatch = true;
+ for (int i=1; i < (int)counts.size(); i++) {
+ if (counts[i] != numDelims) {
+ countsMatch = false;
+ }
+ }
+ if (countsMatch) {
+ //Hurray!! We have successfully found a delimited file.
+ _isDelimited = true;
+ _delimChar = suspectChar;
+ _numFields = numDelims +1;
+ return true;
+ } else {
+ return false;
+ }
+ }
+ return false;
+}
+
+
+void FileRecordTypeChecker::setBam()
+{
+ _fileType = BAM_FILE_TYPE;
+ _recordType = BAM_RECORD_TYPE;
+ _isBinary = true;
+ _isBAM = true;
+}
diff --git a/src/utils/fileType/FileRecordTypeChecker.h b/src/utils/fileType/FileRecordTypeChecker.h
new file mode 100644
index 0000000..6d598ac
--- /dev/null
+++ b/src/utils/fileType/FileRecordTypeChecker.h
@@ -0,0 +1,126 @@
+/*
+ * FileRecordTypeChecker.h
+ *
+ * Created on: Nov 19, 2012
+ * Author: nek3d
+ */
+
+#ifndef FILERECORDTYPECHECKER_H_
+#define FILERECORDTYPECHECKER_H_
+
+using namespace std;
+
+#include <string>
+#include <cstring>
+#include <cstdio>
+#include <cctype>
+#include <cstdlib>
+#include <vector>
+#include <map>
+#include "PushBackStreamBuf.h"
+
+class FileRecordTypeChecker {
+public:
+
+ FileRecordTypeChecker();
+ ~FileRecordTypeChecker() {}
+
+ typedef enum { UNKNOWN_FILE_TYPE, SINGLE_LINE_DELIM_TEXT_FILE_TYPE,
+ MULTI_LINE_ENTRY_TEXT_FILE_TYPE,
+ GFF_FILE_TYPE, GZIP_FILE_TYPE, BAM_FILE_TYPE, VCF_FILE_TYPE} FILE_TYPE;
+
+ typedef enum { UNKNOWN_RECORD_TYPE, BED3_RECORD_TYPE, BED4_RECORD_TYPE, BEDGRAPH_RECORD_TYPE, BED5_RECORD_TYPE,
+ BED6_RECORD_TYPE, BED12_RECORD_TYPE, BED_PLUS_RECORD_TYPE, BAM_RECORD_TYPE, VCF_RECORD_TYPE, GFF_RECORD_TYPE} RECORD_TYPE;
+
+ void setFilename(const QuickString & filename) { _filename = filename; }
+ bool scanBuffer(const char *buf, size_t len=0);
+ bool needsMoreData() const { return _insufficientData; }
+
+ bool recordTypeHasName(RECORD_TYPE type) const { return _hasName.find(type) != _hasName.end(); }
+ bool recordTypeHasScore(RECORD_TYPE type) const { return _hasScore.find(type) != _hasScore.end(); }
+ bool recordTypeHasStrand(RECORD_TYPE type) const { return _hasStrand.find(type) != _hasStrand.end(); }
+
+ FILE_TYPE getFileType() const { return _fileType; }
+ RECORD_TYPE getRecordType() const { return _recordType; }
+ const string &getFileTypeName() const {
+ return _fileTypeNames.find(_fileType)->second;
+ }
+ const string &getRecordTypeName() const {
+ return _recordTypeNames.find(_recordType)->second;
+ }
+
+ bool isBinary() const { return _isBinary; }
+ bool isBam() const { return _isBAM; }
+ bool isGzipped() const { return _isGzipped; }
+
+ void setBam(); //call only if you're SURE the file is BAM!
+
+
+ bool isText() const { return _isText; }
+ bool isDelimited() const { return _isDelimited; }
+ char getDelimChar() const { return _delimChar; }
+ int getNumFields() const { return _numFields; }
+
+ bool isVcf() const;
+ bool isBed() const { return _isBed; }
+ bool isBed3() const { return (_isBed && _numFields == 3); }
+ bool isBed4() const { return (_isBed && _numFields == 4 && !_fourthFieldNumeric); }
+ bool isBedGraph() const { return (_isBed && _numFields == 4 && _fourthFieldNumeric); }
+ bool isBed5() const { return (_isBed && _numFields == 3); }
+ bool isBed6() const { return (_isBed && _numFields == 6); }
+ bool isBedPlus() const { return (_isBed && _numFields > 6 && _numFields != 12); }
+ bool isBed12() const { return (_isBed && _numFields == 12); }
+ bool isGFF() const { return _isGFF; }
+
+
+
+
+
+
+private:
+ FILE_TYPE _fileType;
+ RECORD_TYPE _recordType;
+
+ QuickString _filename; //useful for reporting errors with file.
+ vector<QuickString> _lines;
+ vector<QuickString> _currLineElems;
+ int _firstValidDataLineIdx;
+ int _numBytesInBuffer; //this will hold the length of the buffer after the scan.
+
+ int _numFields;
+ bool _isBinary;
+ bool _isText;
+ bool _isBed;
+ bool _isDelimited;
+ char _delimChar;
+ bool _isVCF;
+ bool _isBAM;
+ bool _isGFF;
+ bool _isGzipped;
+ bool _insufficientData; //set to true if scan buffer had only header lines.
+ bool _fourthFieldNumeric; //this is just to distinguish between Bed4 and BedGraph files.
+
+ map<RECORD_TYPE, string> _recordTypeNames;
+ map<FILE_TYPE, string> _fileTypeNames;
+
+ map<RECORD_TYPE, bool> _hasName;
+ map<RECORD_TYPE, bool> _hasScore;
+ map<RECORD_TYPE, bool> _hasStrand;
+
+ //this will be used in determining whether we are looking at a binary or text file.
+ static const float PERCENTAGE_PRINTABLE = .9;
+ bool isBinaryBuffer(const char *buffer, size_t len);
+ bool isBAM(const char *buffer);
+ bool handleTextFormat(const char *buffer, size_t len);
+ bool isTextDelimtedFormat(const char *buffer, size_t len);
+ bool isBedFormat();
+ bool isVCFformat(const char *buffer);
+ bool isGFFformat();
+ bool delimiterTesting(vector<int> &counts, char suspectChar);
+
+
+
+
+};
+
+#endif /* FILERECORDTYPECHECKER_H_ */
diff --git a/src/utils/fileType/Makefile b/src/utils/fileType/Makefile
index 91585d5..50ed87b 100644
--- a/src/utils/fileType/Makefile
+++ b/src/utils/fileType/Makefile
@@ -4,26 +4,28 @@ UTILITIES_DIR = ../../utils/
# -------------------
# define our includes
# -------------------
-INCLUDES =
+INCLUDES = -I$(UTILITIES_DIR)/BamTools/include/ \
+ -I$(UTILITIES_DIR)/general
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= fileType.cpp fileType.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= fileType.cpp fileType.h FileRecordTypeChecker.cpp FileRecordTypeChecker.h
+OBJECTS= fileType.o FileRecordTypeChecker.o
+#_EXT_OBJECTS=ParseTools.o QuickString.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) $(INCLUDES)
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
-
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+ @rm -f $(OBJ_DIR)/fileType.o $(OBJ_DIR)/FileRecordTypeChecker.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/general/BTlist.h b/src/utils/general/BTlist.h
new file mode 100644
index 0000000..7bae4f3
--- /dev/null
+++ b/src/utils/general/BTlist.h
@@ -0,0 +1,262 @@
+/*
+ * BTlist.h
+ *
+ * Created on: Jan 18, 2013
+ * Author: nek3d
+ */
+
+#ifndef BT_LIST_H_
+#define BT_LIST_H_
+
+//
+// Writing our own singly linked list template class because:
+//
+// 1) STL doesn't currently support one that I can find without
+// C++0x support or SGI extensions.
+//
+// 2) A normal singly linked list doesn't support constant time
+// insertion or deletion at the end. It also doesn't track
+// your current position or let you delete at that position,
+// but this does.
+//
+// 3) A normal STL list is doubly-linked, which would do all
+// these things, but more slowly and with more memory.
+//
+// 4) I can.
+
+
+#include "FreeList.h"
+#include "QuickString.h"
+#include <stack>
+#include <cstring> //for memset
+
+template <class T> class BTlist;
+
+template <class T>
+class BTlistNode {
+public:
+ friend class BTlist<T>;
+
+ BTlistNode() : _next(NULL){}
+ BTlistNode(const T &val) : _val(val), _next(NULL) {}
+ const T &value() const { return _val; }
+ const BTlistNode<T> *next() const { return _next; }
+ BTlistNode<T> *next() { return _next; }
+ bool hasNext() const { return _next != NULL; }
+ void clear() {
+ _next = NULL;
+ //for the value, set numbers to 0, ptrs to NULL, etc.
+ memset((void *)_val, 0, sizeof(T));
+ }
+
+private:
+
+ T _val;
+ BTlistNode *_next;
+};
+
+template <class T> class BTlist {
+public:
+ BTlist() :
+ _begin(NULL),
+ _currEnd(NULL),
+ _prevCursor(NULL),
+ _size(0),
+ _dontDelete(false)
+ {
+ }
+ //This version of the constructor will convert a QuickString into a BTlist.
+ //It is effectively the opposite of the toStr method.
+ BTlist(const QuickString &str) :
+ _begin(NULL),
+ _currEnd(NULL),
+ _prevCursor(NULL),
+ _size(0),
+ _dontDelete(false)
+ {
+ for (int i=0; i < (int)str.size(); i++) {
+ push_back((T)(str[i]));
+ }
+ }
+
+ ~BTlist() {
+ clear();
+ }
+
+ typedef const BTlistNode<T> * const_iterator_type;
+
+ bool empty() const { return _begin == NULL; }
+ size_t size() const { return _size; }
+
+ const BTlistNode<T> *front() const { return _begin;}
+ BTlistNode<T> *back() const { return _currEnd; }
+ void pop_front() {
+ if (empty()) {
+ return;
+ }
+ BTlistNode<T> *killNode = _begin;
+ if (_begin->_next == NULL) { //this is the only item. List is 1.
+ delete killNode;
+ _begin = NULL;
+ _currEnd = NULL;
+ _prevCursor = NULL;
+ _size = 0;
+ return;
+ }
+ if (_prevCursor == _begin) {
+ _prevCursor = _begin->_next;
+ }
+ _begin = _begin->next();
+ delete killNode;
+ _size--;
+ }
+
+ const BTlistNode<T> *begin() {
+ _prevCursor = NULL;
+ return _begin;
+ }
+
+ const BTlistNode<T> *begin() const {
+ return _begin;
+ }
+ const BTlistNode<T> *next() {
+ if (_prevCursor == NULL) {
+ _prevCursor = _begin;
+ return _begin->_next;
+ }
+ _prevCursor = _prevCursor->_next;
+ return _prevCursor->_next;
+ }
+ const BTlistNode<T> *end() const { return NULL; }
+
+ BTlistNode<T> * deleteCurrent() {
+ //delete what the current cursor is pointing to,
+ //meaning whatever the prevCursor's next member points to.
+ BTlistNode<T> *returnNode = NULL;
+ BTlistNode<T> *killNode = NULL;
+ if (_prevCursor == NULL) {
+ //deleting first item in list.
+ killNode = _begin;
+ _begin = _begin->_next;
+ returnNode = _begin;
+
+ } else {
+ killNode = _prevCursor->_next;
+ _prevCursor->_next = _prevCursor->_next->_next;
+ returnNode = _prevCursor->_next;
+ }
+ if (_currEnd == killNode) {
+ //deleting last item in list
+ _currEnd = _prevCursor; //back up the current end.
+ }
+ delete killNode;
+ _size--;
+
+ return returnNode;
+ }
+
+ void push_back(const T &val) {
+ BTlistNode<T> *newNode = new BTlistNode<T>(val);
+ if (empty()) {
+ _begin = newNode;
+ _currEnd = newNode;
+ _prevCursor = NULL;
+ } else {
+ _currEnd->_next = newNode;
+ _prevCursor = _currEnd;
+ _currEnd = newNode;
+ }
+ _size++;
+ }
+
+// void push_front(const T &val) {
+// BTlistNode<T> *newNode = new BTlistNode<T>(val);
+// if (empty()) {
+// _begin = newNode;
+// _currEnd = newNode;
+// _prevCursor = NULL;
+// } else {
+// newNode->_next = _begin;
+// _begin = newNode;
+// _prevCursor = _currEnd;
+// }
+// _size++;
+// }
+// void push_front(BTlist<T> &newList) {
+// stack<T> theStack;
+// for (const_iterator_type iter = newList.begin(); iter != newList.end(); iter = newList.next()) {
+// theStack.push(iter->_val);
+// }
+// while (!theStack.empty()) {
+// const T &val = theStack.top();
+// theStack.pop();
+// push_front(val);
+// }
+// }
+
+ void clear() {
+ if (_dontDelete) {
+ return;
+ }
+ //delete all nodes, set cursors to NULL, set size to 0.
+ BTlistNode<T> *killNode = _begin;
+ while (killNode != NULL) {
+ BTlistNode<T> *nextNode = killNode->_next;
+ delete killNode;
+ killNode = nextNode;
+ }
+ _begin = NULL;
+ _currEnd = NULL;
+ _prevCursor = NULL;
+ _size = 0;
+ }
+
+ const BTlist<T> &operator=(const BTlist<T> &other) {
+ //need to make copies of all nodes and assign values
+ clear();
+
+ BTlistNode<T> *node = other._begin;
+ while (node != NULL) {
+ push_back(node->_val);
+ node = node->_next;
+ }
+ return *this;
+ }
+ void assignNoCopy(BTlist<T> &other) {
+ _begin = other._begin;
+ _size = other._size;
+ _currEnd = other._currEnd;
+ _prevCursor = other._prevCursor;
+ _dontDelete = true;
+ }
+
+ //this method will convert the contents of the list into a QuickString.
+ //It assumes that the templated type of the listNode can be converted to a
+ //char using the (char) cast. The user must ensure that this is the case.
+ //The 2nd parameter needs only be true if you wish to append the data
+ //to the QuickString's existing contents. Otherwise, it will be cleared first.
+ void toStr(QuickString &str, bool append = false) const {
+ if (!append) {
+ str.clear();
+ }
+ str.reserve(_size + str.size());
+ for (const BTlistNode<T> *iter = begin(); iter != end(); iter = iter->next()) {
+ str.append((char)iter->value());
+ }
+ }
+
+private:
+ BTlistNode<T> *_begin;
+ //keep a cursor to the last element for constant time push_back and pop_back functions.
+ BTlistNode<T> *_currEnd;
+ BTlistNode<T> *_prevCursor;
+ size_t _size;
+
+ bool _dontDelete; //this will usally be false, but set to true when
+ //calling assignNoCopy, as our list will actually just be a pointer
+ //to another list.
+
+
+};
+
+#endif /* BT_LIST_H_ */
diff --git a/src/utils/general/BedtoolsTypes.h b/src/utils/general/BedtoolsTypes.h
new file mode 100644
index 0000000..46aef49
--- /dev/null
+++ b/src/utils/general/BedtoolsTypes.h
@@ -0,0 +1,33 @@
+/*
+ * BedtoolsTypes.h
+ *
+ * Created on: Feb 13, 2013
+ * Author: nek3d
+ */
+
+#ifndef BEDTOOLSTYPES_H_
+#define BEDTOOLSTYPES_H_
+
+using namespace std;
+
+#include <stdint.h>
+#include <climits>
+#include <string>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
+#include <iostream>
+#include "QuickString.h"
+
+//STL headers
+#include <utility> //include pair and make_pair
+#include <vector>
+#include <set>
+#include <map>
+
+
+typedef uint32_t CHRPOS;
+
+
+
+#endif /* BEDTOOLSTYPES_H_ */
diff --git a/src/utils/general/CompressionTools.cpp b/src/utils/general/CompressionTools.cpp
new file mode 100644
index 0000000..a29d35a
--- /dev/null
+++ b/src/utils/general/CompressionTools.cpp
@@ -0,0 +1,45 @@
+/*
+ * CompressionTools.cpp
+ *
+ * Created on: Apr 10, 2013
+ * Author: nek3d
+ */
+
+#include "CompressionTools.h"
+#include <cstring> //for strlen
+
+unsigned long inflateGzippedArray(const BTlist<int> &inList, unsigned char* outbuf, size_t outbufSize, size_t inbufSize)
+{
+ if (inbufSize == 0) {
+ inbufSize = inList.size();
+ }
+ Bytef *inbuf = new Bytef[inbufSize +1];
+ memset(inbuf, 0, inbufSize +1);
+
+ int i=0;
+ for (BTlist<int>::const_iterator_type iter = inList.begin(); iter != inList.end(); iter = iter->next()) {
+ inbuf[i] = iter->value();
+ i++;
+ }
+ // zlib struct
+ z_stream infstream;
+ infstream.zalloc = Z_NULL;
+ infstream.zfree = Z_NULL;
+ infstream.opaque = Z_NULL;
+ // setup "b" as the input and "c" as the compressed output
+ infstream.avail_in = inbufSize; // size of input
+ infstream.next_in = (Bytef *)inbuf; // input char array
+ infstream.avail_out = outbufSize; // size of output
+ infstream.next_out = (Bytef *)outbuf; // output char array
+
+ // the actual DE-compression work.
+ inflateInit2(&infstream, 16+MAX_WBITS); //decompresses gzipped data instead of zlib compressed data.
+ inflate(&infstream, Z_NO_FLUSH);
+ inflateEnd(&infstream);
+
+ delete [] inbuf;
+
+ return infstream.total_out;
+
+}
+
diff --git a/src/utils/general/CompressionTools.h b/src/utils/general/CompressionTools.h
new file mode 100644
index 0000000..8b41336
--- /dev/null
+++ b/src/utils/general/CompressionTools.h
@@ -0,0 +1,25 @@
+/*
+ * CompressionTools.h
+ *
+ * Created on: Apr 10, 2013
+ * Author: nek3d
+ */
+
+#ifndef COMPRESSIONTOOLS_H_
+#define COMPRESSIONTOOLS_H_
+
+using namespace std;
+
+#include <zlib.h>
+#include "BTlist.h"
+
+//pass an array of gzipped data, and an empty, PRE-ALLOCATED buffer to store the unzipped results.
+//return value is the length of the uncompressed data.
+unsigned long inflateGzippedArray(const BTlist<int> &inbuf, //the input. Gzipped data.
+ unsigned char* outbuf, //user must allocate enough space for uncompressed output!
+ size_t outbufSize, //capacity of output buffer
+ size_t inbufSize =0); //save time on call to strlen by providing size of inbuf.
+
+
+
+#endif /* COMPRESSIONTOOLS_H_ */
diff --git a/src/utils/general/DualQueue.h b/src/utils/general/DualQueue.h
new file mode 100644
index 0000000..1cee415
--- /dev/null
+++ b/src/utils/general/DualQueue.h
@@ -0,0 +1,124 @@
+/*
+ * DualQueue.h
+ *
+ * Created on: Jan 29, 2013
+ * Author: nek3d
+ */
+#ifdef false
+#ifndef DUALQUEUE_H_
+#define DUALQUEUE_H_
+
+using namespace std;
+
+#include <vector>
+#include <queue>
+#include <cstdio>
+#include <cstdlib>
+
+template <class T> class DualQueueAscending {
+public:
+ bool operator() ( const T &item1, const T &item2) const {
+
+ printf("\n\nIn comparison method:\n item1=\n");
+// item1->print();
+ printf("\nitem2=\n");
+// item2->print();
+ printf("\n");
+
+ if( *(item1) < *(item2) ) {
+ printf("Item1 less than item2. Returning false.\n");
+ return false;
+ }
+ printf("Item1 not less than item2. Returning true.\n");
+ return true;
+ }
+};
+
+template <class T> class DualQueueDescending {
+public:
+ bool operator() ( const T &item1, const T &item2) const {
+ if( *(item2) < *(item1) ) {
+ return false;
+ }
+ return true;
+ }
+};
+
+
+template <class T, template<class T> class CompareFunc> class DualQueue {
+public:
+ DualQueue() {}
+ ~DualQueue() {}
+
+ const T & top() const {
+ if (empty()) {
+ fprintf(stderr, "ERROR. Tried to top from empty dualQueue.\n");
+ exit(1);
+ }
+ if (emptyForward()) {
+ return topReverse();
+ }
+ if (emptyReverse()) {
+ return topForward();
+ }
+
+ return (topFowardHigherPriorityThanTopReverse() ? topForward() : topReverse());
+ }
+ void pop() {
+ if (empty()) {
+ fprintf(stderr, "ERROR. Tried to pop from empty dualQueue.\n");
+ exit(1);
+ }
+ if (emptyForward()) {
+ popReverse();
+ return;
+ }
+ if (emptyReverse()) {
+ popForward();
+ return;
+ }
+ topFowardHigherPriorityThanTopReverse() ? popForward() : popReverse();
+ }
+ void push(const T &item) { item->getStrand() ? pushForward(item) : pushReverse(item); }
+ size_t size() const { return sizeForward() + sizeReverse(); }
+ bool empty() const { return _forwardQueue.empty() && _reverseQueue.empty(); }
+
+ const T & topForward() const { return _forwardQueue.top(); }
+ void popForward() { _forwardQueue.pop(); }
+ void pushForward(const T &item) { _forwardQueue.push(item); }
+ size_t sizeForward() const { return _forwardQueue.size(); }
+ bool emptyForward() const { return _forwardQueue.empty(); }
+
+
+ const T & topReverse() const { return _reverseQueue.top(); }
+ void popReverse() { _reverseQueue.pop(); }
+ void pushReverse(const T &item) { _reverseQueue.push(item); }
+ size_t sizeReverse() const { return _reverseQueue.size(); }
+ bool emptyReverse() const { return _reverseQueue.empty(); }
+
+
+private:
+ typedef priority_queue<T, vector<T>, CompareFunc<T> > queueType;
+ queueType _forwardQueue;
+ queueType _reverseQueue;
+
+ bool topFowardHigherPriorityThanTopReverse() const {
+ printf("\n\nIn priority method:\n TopForward=\n");
+// topForward()->print();
+ printf("\nTopReverse=\n");
+// topReverse()->print();
+ printf("\n");
+ if (CompareFunc<T>()(topForward(), topReverse())) {
+ printf("Forward higher priority than reverse.\n");
+ return true;
+ } else {
+ printf("Reverse higher priority than forward.\n");
+ return false;
+ }
+ }
+
+};
+
+
+#endif /* DUALQUEUE_H_ */
+#endif
diff --git a/src/utils/general/ErrorMsg.h b/src/utils/general/ErrorMsg.h
new file mode 100644
index 0000000..e595402
--- /dev/null
+++ b/src/utils/general/ErrorMsg.h
@@ -0,0 +1,14 @@
+/*
+ * ErrorMsg.h
+ *
+ * Created on: Feb 13, 2013
+ * Author: nek3d
+ */
+
+#ifndef ERRORMSG_H_
+#define ERRORMSG_H_
+
+
+
+
+#endif /* ERRORMSG_H_ */
diff --git a/src/utils/general/FreeList.h b/src/utils/general/FreeList.h
new file mode 100644
index 0000000..4aaa6f5
--- /dev/null
+++ b/src/utils/general/FreeList.h
@@ -0,0 +1,83 @@
+/*
+ * FreeList.h
+ *
+ * Created on: Nov 30, 2012
+ * Author: nek3d
+ */
+
+#ifndef FREELIST_H_
+#define FREELIST_H_
+
+using namespace std;
+
+#include <cstddef> //defines NULL
+#include <deque>
+#include <vector>
+
+template <class T>
+class FreeList {
+public:
+ FreeList(int blockSize=512)
+ : _nextPos(0),
+ _blockSize(blockSize)
+ {
+ _freeList.reserve(_blockSize);
+ }
+
+ ~FreeList() {
+ for (int i=0; i < (int)_buffer.size(); i++) {
+ delete _buffer[i];
+ }
+ }
+
+ void clear() {
+ _nextPos = 0;
+ _freeList.clear();
+ }
+
+ T *newObj() {
+ T *ptr = NULL;
+
+ if (_freeList.size() > 0) {
+ ptr = _freeList.back();
+ _freeList.pop_back();
+ } else {
+ if (_nextPos == (int)_buffer.size()) {
+ growBuffer();
+ }
+ ptr = _buffer[_nextPos];
+ _nextPos ++;
+ }
+
+ return ptr;
+ }
+
+ void deleteObj(const T *ptr) {
+ if (ptr != NULL) {
+ T *volatilePtr = const_cast<T *>(ptr); //remove const-ness.
+ volatilePtr->clear();
+ _freeList.push_back(volatilePtr);
+ }
+ }
+
+ int capacity() const { return _buffer.size(); }
+
+private:
+ deque<T *> _buffer;
+ vector<T *> _freeList;
+ int _nextPos;
+ int _blockSize;
+ void growBuffer() {
+ for (int i=0; i < _blockSize; ++i) {
+ _buffer.push_back(new T());
+ }
+ }
+
+ //this number determines how many times larger than the blockSize the freeList
+ //is allowed to grow. If speed performance is poor, we may need to increase this number.
+ //If memory performance is poor, decrease it.
+ static const int MAX_MULTIPLE_FREE_LIST_SIZE = 10;
+};
+
+
+#endif /* FREELIST_H_ */
diff --git a/src/utils/general/InflateStreamBuf.h b/src/utils/general/InflateStreamBuf.h
new file mode 100644
index 0000000..7c37339
--- /dev/null
+++ b/src/utils/general/InflateStreamBuf.h
@@ -0,0 +1,130 @@
+/*
+ * InflateStreamBuf.h
+ *
+ * Created on: Apr 11, 2013
+ * Author: nek3d
+ */
+
+#ifndef INFLATESTREAMBUF_H_
+#define INFLATESTREAMBUF_H_
+
+using namespace std;
+
+#include <iostream>
+#include <cstdio>
+#include <cerrno>
+#include <cstring>
+#include <zlib.h>
+#include <cstdlib>
+
+#define GZBUFSIZ BUFSIZ
+
+class InflateStreamBuf:public std::streambuf
+{
+public:
+ InflateStreamBuf(std::istream* in):in(in),status_flag(0) {
+ if(in==NULL) throw ("Null pointer");
+ std::memset((void*)&strm,0,sizeof(z_stream));
+ strm.zalloc = Z_NULL;
+ strm.zfree = Z_NULL;
+ strm.opaque = Z_NULL;
+ strm.avail_in = 0;
+ strm.next_in = Z_NULL;
+
+ buffer=(char*)std::malloc(GZBUFSIZ*sizeof(char));
+ if(buffer==NULL) {
+ throw ("out of memory");
+ }
+ if ( inflateInit2(&strm, 16+MAX_WBITS) != Z_OK) {
+ throw ("::inflateInit failed");
+ }
+ setg(&buffer[0], &buffer[GZBUFSIZ], &buffer[GZBUFSIZ]);
+ }
+
+ virtual void close() {
+ if(in!=NULL) {
+ in=NULL;
+ (void)inflateEnd(&strm);
+ free(buffer);
+ buffer=NULL;
+ }
+ in=NULL;
+ }
+
+ virtual ~InflateStreamBuf() {
+ close();
+ }
+
+ virtual int underflow () {
+
+ if(in==NULL) return EOF;
+ if(status_flag == Z_STREAM_END) {
+ close();
+ return EOF;
+ }
+ in->read((char*)buffin, GZBUFSIZ);
+
+ strm.avail_in = in->gcount();
+
+ if(strm.avail_in == 0) {
+ close();
+ return EOF;
+ }
+ strm.next_in=buffin;
+ /* run inflate() on input until output buffer not full */
+ unsigned int total=0;
+ _currentOutBufSize = 0;
+ do {
+ strm.avail_out = GZBUFSIZ;
+ strm.next_out = buffout;
+ status_flag = ::inflate(&strm, Z_NO_FLUSH);
+
+ switch (status_flag) {
+ case 0:break;
+ case Z_STREAM_END:break;
+ case Z_NEED_DICT:
+ status_flag=Z_DATA_ERROR;
+ case Z_DATA_ERROR:
+ case Z_MEM_ERROR:
+
+ close();
+ throw status_flag;
+ break;
+ default:
+ {
+ close();
+ throw status_flag;
+ break;
+ }
+ }
+
+ unsigned int have = GZBUFSIZ - strm.avail_out;
+ buffer=(char*)std::realloc(buffer,sizeof(char)*(total+have));
+ if(buffer==NULL) {
+ throw ("out of memory");
+ }
+
+ memcpy((void*)&buffer[total], &buffout[0], sizeof(char)*have);
+ total+=have;
+ } while (strm.avail_out == 0 && strm.avail_in > 0);
+
+
+ setg(buffer, buffer, &buffer[total]);
+ _currentOutBufSize = total;
+
+ return total==0?EOF:this->buffer[0];
+ }
+
+protected:
+ std::istream* in;
+ unsigned char buffin[GZBUFSIZ];
+ unsigned char buffout[GZBUFSIZ];
+ char* buffer;
+ z_stream strm;
+ int status_flag;
+ int _currentOutBufSize;
+};
+
+
+
+#endif /* INFLATESTREAMBUF_H_ */
diff --git a/src/utils/fileType/Makefile b/src/utils/general/Makefile
similarity index 56%
copy from src/utils/fileType/Makefile
copy to src/utils/general/Makefile
index 91585d5..43dcfba 100644
--- a/src/utils/fileType/Makefile
+++ b/src/utils/general/Makefile
@@ -9,21 +9,20 @@ INCLUDES =
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= fileType.cpp fileType.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+SOURCES= QuickString.h QuickString.cpp ParseTools.h ParseTools.cpp PushBackStreamBuf.cpp PushBackStreamBuf.h CompressionTools.h CompressionTools.cpp
+OBJECTS= QuickString.o ParseTools.o PushBackStreamBuf.o CompressionTools.o
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) $(INCLUDES)
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
-
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+ @rm -f $(OBJ_DIR)/QuickString.o $(OBJ_DIR)/ParseTools.o $(OBJ_DIR)/PushBackStreamBuf.o
-.PHONY: clean
\ No newline at end of file
+.PHONY: clean
diff --git a/src/utils/general/ParseTools.cpp b/src/utils/general/ParseTools.cpp
new file mode 100644
index 0000000..ad5764b
--- /dev/null
+++ b/src/utils/general/ParseTools.cpp
@@ -0,0 +1,143 @@
+#include "ParseTools.h"
+#include <climits>
+#include <cctype>
+#include <cstring>
+
+//This functions recognizes only numbers with digits, plus sign, minus sign, decimal point, e, or E. Hexadecimal and pointers not currently supported.
+bool isNumeric(const QuickString &str) {
+ for (int i=0; i < (int)str.size(); i++) {
+ char currChar = str[i];
+ if (!(isdigit(currChar) || currChar == '-' || currChar == '.' || currChar == '+' || currChar == 'e' || currChar == 'E')) {
+ return false;
+ }
+ }
+ return true;
+}
+
+int str2chrPos(const QuickString &str) {
+ return str2chrPos(str.c_str(), str.size());
+}
+
+int str2chrPos(const char *str, size_t ulen) {
+ int len=(int)ulen;
+ if (len < 1 || len > 10) {
+ return INT_MIN; //can't do more than 9 digits and a minus sign
+ }
+
+ register int sum=0;
+ int startPos =0;
+ bool isNegative = false;
+
+ //check for negative numbers
+ if (str[0] == '-') {
+ isNegative = true;
+ startPos = 1;
+ }
+
+ for (int i=startPos; i < len; i++) {
+ char currChar = str[i];
+ if (!isdigit(currChar)) {
+ return INT_MIN;
+ }
+ int dig = currChar - 48; //ascii code for zero.
+ int power = len -i -1;
+
+ switch (power) {
+ case 0:
+ sum += dig;
+ break;
+ case 1:
+ sum += dig * 10;
+ break;
+ case 2:
+ sum += dig *100;
+ break;
+ case 3:
+ sum += dig *1000;
+ break;
+ case 4:
+ sum += dig *10000;
+ break;
+ case 5:
+ sum += dig *100000;
+ break;
+ case 6:
+ sum += dig *1000000;
+ break;
+ case 7:
+ sum += dig *10000000;
+ break;
+ case 8:
+ sum += dig *100000000;
+ break;
+ case 9:
+ sum += dig *1000000000;
+ break;
+ default:
+ return INT_MIN;
+ break;
+ }
+ }
+ return isNegative ? 0 - sum : sum;
+}
+
+string vectorIntToStr(const vector<int> &vec) {
+ string str;
+ str.reserve(vec.size());
+ for (int i=0; i < (int)vec.size(); i++) {
+ str += (char)(vec[i]);
+ }
+ return str;
+}
+
+// TBD: Could be better optimized. I'm allocating 8KB for every call, then destroying it.
+// That memory needs to stay in scope.
+// Also, is this handling subsequent delimiters?
+int Tokenize(const QuickString &str, vector<QuickString> &elems, char delimiter, int numExpectedItems) {
+
+ elems.reserve(numExpectedItems);
+ int strLen = (int)str.size();
+
+ int startPos = 0;
+ int currPos = 0;
+
+ char elemBuf[8192];
+
+ while (startPos < strLen) {
+ memset(elemBuf, 0, 8192);
+ while (str[currPos] != delimiter && currPos < strLen) {
+ currPos++;
+ }
+ if (currPos > startPos) {
+ memcpy(elemBuf, str.c_str() + startPos, min(currPos, strLen) - startPos);
+ elems.push_back(elemBuf);
+ }
+ startPos = currPos +1;
+ currPos = startPos;
+ }
+ return (int)elems.size();
+}
+
+bool isHeaderLine(QuickString &line) {
+ if (line[0] == '>') {
+ return true;
+ }
+ if (line[0] == '!') {
+ return true;
+ }
+ if (line[0] == '#') {
+ return true;
+ }
+ //GFF file headers can also start with the words "browser" or "track", followed by a whitespace character.
+ if (memcmp(line.c_str(), "browser", 7) == 0 && isspace(line[7])) {
+ return true;
+ }
+ if (memcmp(line.c_str(), "track", 5) == 0 && isspace(line[5])) {
+ return true;
+ }
+ if (memcmp(line.c_str(), "visibility", 10) == 0) {
+ return true;
+ }
+ return false;
+}
+
diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
new file mode 100644
index 0000000..2132d0e
--- /dev/null
+++ b/src/utils/general/ParseTools.h
@@ -0,0 +1,97 @@
+/*
+ * parseTools.h
+ *
+ * Created on: Dec 3, 2012
+ * Author: nek3d
+ */
+
+#ifndef PARSETOOLS_H_
+#define PARSETOOLS_H_
+
+using namespace std;
+
+#include <cstring> //for memset
+#include <string>
+#include <vector>
+#include "QuickString.h"
+
+bool isNumeric(const QuickString &str);
+
+//This method is a faster version of atoi, but is limited to a maximum of
+//9 digit numbers in Base 10 only. The string may begin with a negative.
+//Empty strings, too long strings, or strings containing anything other than
+//digits (with the excpetion of a minus sign in the first position)
+//will result in error. Errors return INT_MIN.
+int str2chrPos(const char *str, size_t len);
+int str2chrPos(const QuickString &str);
+
+
+//int2str is faster but less flexible version of the ToString method in
+//lineFileUtilities. Unlike ToString, which uses streams, this method
+//can only handle integers. The buffer, which is templated, needs to support the
+//assignment operater for char *, meaning it needs a T::operator = (const char *) method.
+//strings, QuickStrings, stringbuffers, and the like are acceptable.
+
+template<class T>
+void int2str(int number, T& buffer, bool appendToBuf = false)
+{
+
+ register int useNum = number;
+ if (useNum == 0) {
+ if (appendToBuf) {
+ buffer.append("0");
+ } else {
+ buffer = "0";
+ }
+ return;
+ }
+ //check for negative numbers.
+ bool isNegative = useNum < 0;
+ if (isNegative) {
+ useNum = 0 - useNum; //convert to positive.
+ }
+
+ //figure out how many digits we have
+ register int power = 10;
+ int numChars = 2 + (isNegative ? 1: 0);
+ while (power <= useNum) {
+ power *= 10;
+ numChars++;
+ }
+
+ char tmpBuf[numChars];
+ memset(tmpBuf, 0, numChars);
+
+ int bufIdx=0;
+ if (isNegative) {
+ tmpBuf[0] = '-';
+ bufIdx = 1;
+ }
+ register int currDig=0;
+
+ power /= 10;
+ while (power) {
+
+ currDig = useNum / power;
+ useNum -= currDig * power;
+ tmpBuf[bufIdx] = currDig + 48; //48 is ascii for zero.
+ bufIdx++;
+ power /= 10;
+ }
+ if (!appendToBuf) {
+ buffer = tmpBuf;
+ } else {
+ buffer.append(tmpBuf, numChars-1);
+ }
+
+}
+
+bool isHeaderLine(QuickString &line);
+
+string vectorIntToStr(const vector<int> &vec);
+
+
+//This is a faster version of tokenize that doesn't use strings. Return value is final size of elems vector.
+int Tokenize(const QuickString &str, vector<QuickString> &elems, char delimiter = '\t', int numExpectedItems = 0);
+
+#endif /* PARSETOOLS_H_ */
diff --git a/src/utils/general/PushBackStreamBuf.cpp b/src/utils/general/PushBackStreamBuf.cpp
new file mode 100644
index 0000000..a4c1285
--- /dev/null
+++ b/src/utils/general/PushBackStreamBuf.cpp
@@ -0,0 +1,51 @@
+/*
+ * PushBackStream.cpp
+ *
+ * Created on: Mar 18, 2013
+ * Author: nek3d
+ */
+#include <cstdio>
+
+#include "PushBackStreamBuf.h"
+#include <cstring>
+#include <iostream>
+
+PushBackStreamBuf::PushBackStreamBuf(streambuf* primary_stream)
+: streambuf(),
+ _primary_stream(primary_stream)
+ {
+
+}
+
+PushBackStreamBuf::~PushBackStreamBuf()
+{
+}
+
+int PushBackStreamBuf::sbumpc()
+ {
+ int c = 0;
+ if (!_buffer.empty()) {
+ c = _buffer.front()->value();
+ _buffer.pop_front();
+ return c;
+ }
+ c = _primary_stream->sbumpc();
+ return c;
+}
+
+void PushBackStreamBuf::pushBack(const BTlist<int> &newBuf)
+{
+ _buffer = newBuf;
+}
+
+int PushBackStreamBuf::underflow()
+{
+ int c = 0;
+
+ if(!_buffer.empty()) {
+ c=_buffer.front()->value();
+ return c;
+ }
+ c= _primary_stream->sgetc();
+ return c;
+}
diff --git a/src/utils/general/PushBackStreamBuf.h b/src/utils/general/PushBackStreamBuf.h
new file mode 100644
index 0000000..0c41cd5
--- /dev/null
+++ b/src/utils/general/PushBackStreamBuf.h
@@ -0,0 +1,39 @@
+/*
+ * PushBackStream.h
+ *
+ * Created on: Mar 18, 2013
+ * Author: nek3d
+ */
+
+#ifndef PUSHBACKSTREAM_H_
+#define PUSHBACKSTREAM_H_
+
+using namespace std;
+
+#include <iostream>
+#include "BTlist.h"
+
+class PushBackStreamBuf: public std::streambuf {
+public:
+ friend class InputStreamMgr;
+ PushBackStreamBuf(streambuf* primary_stream);
+ ~PushBackStreamBuf();
+ void pushBack(const BTlist<int> &vec);
+// void push_front(const BTlist<int> &vec) { _buffer.push_front(vec); }
+
+ int sbumpc();
+ void clear() { _buffer.clear(); }
+protected:
+ int uflow() { return sbumpc(); }
+
+ int underflow();
+
+private:
+ streambuf* _primary_stream;
+ BTlist<int> _buffer;
+ static const int SCAN_BUFFER_SIZE = 8192; //8 KB buffer
+ static const int MAIN_BUFFER_SIZE = 128 * 1024; //128K buffer
+};
+
+
+#endif /* PUSHBACKSTREAM_H_ */
diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
new file mode 100644
index 0000000..831f84a
--- /dev/null
+++ b/src/utils/general/QuickString.cpp
@@ -0,0 +1,230 @@
+#include "QuickString.h"
+#include <cstring>
+#include <cstdlib>
+#include <cstdio>
+#include "ParseTools.h"
+
+QuickString::QuickString(size_t capacity)
+: _buffer(NULL),
+ _currCapacity(capacity),
+ _currSize(0)
+{
+ build();
+}
+
+QuickString::QuickString(const QuickString &qs)
+: _buffer(NULL),
+ _currCapacity(qs._currCapacity),
+ _currSize(0)
+{
+ build();
+ set(qs._buffer, qs._currSize);
+}
+
+QuickString::QuickString(const char *inBuf)
+{
+ size_t len = strlen(inBuf);
+ _currCapacity = len +1;
+
+ build();
+ set(inBuf, len);
+}
+
+QuickString::QuickString(const string &inString)
+{
+ size_t len = (int)inString.size();
+ _currCapacity = len +1;
+
+ build();
+ set(inString.c_str(), len);
+}
+
+QuickString::QuickString(char c)
+{
+ _currCapacity =2;
+
+ build();
+
+ char buffer[2];
+ buffer[0] = c;
+ buffer[1] = 0;
+
+ set(buffer, 1);
+}
+
+void QuickString::build() {
+ _buffer = (char *)malloc(_currCapacity);
+ clear();
+}
+
+QuickString::~QuickString(){
+ free(_buffer);
+}
+
+void QuickString::clear() {
+ memset(_buffer, 0, _currCapacity);
+ _currSize = 0;
+}
+
+
+QuickString &QuickString::operator = (const char *inBuf){
+ set(inBuf, strlen(inBuf));
+ return *this;
+}
+
+QuickString &QuickString::operator = (const string & inBuf){
+ set(inBuf.c_str(), (int)inBuf.size());
+ return *this;
+}
+
+QuickString &QuickString::operator = (const QuickString & inBuf){
+ set(inBuf._buffer, (int)inBuf._currSize);
+ return *this;
+}
+
+
+QuickString &QuickString::operator += (const QuickString & inBuf)
+{
+ append(inBuf._buffer, (int)inBuf._currSize);
+ return *this;
+}
+
+QuickString &QuickString::operator +=(const string &inBuf)
+{
+ append(inBuf.c_str(), (int)inBuf.size());
+ return *this;
+}
+
+QuickString &QuickString::operator +=(char c) {
+
+ append(c);
+ return *this;
+}
+
+QuickString &QuickString::operator += (const char *inBuf)
+{
+ append(inBuf, strlen(inBuf));
+ return *this;
+}
+
+bool QuickString::operator == (const QuickString &qs) const {
+ if ( _currSize != qs._currSize) {
+ return false;
+ }
+ for (int i= _currSize-1; i > -1; i--) {
+ if (_buffer[i] != qs._buffer[i]) return false;
+ }
+ return true;
+}
+
+bool QuickString::operator == (const string &str) const {
+ if ( _currSize != str.size()) {
+ return false;
+ }
+ for (int i= _currSize-1; i > -1; i--) {
+ if (_buffer[i] != str[i]) return false;
+ }
+ return true;
+
+}
+
+bool QuickString::operator == (const char *str) const {
+ size_t inLen = strlen(str);
+ if (inLen != _currSize) {
+ return false;
+ }
+ for (int i= _currSize-1; i > -1; i--) {
+ if (_buffer[i] != str[i]) return false;
+ }
+ return true;
+}
+
+
+bool QuickString::operator != (const QuickString &qs) const {
+ return !(*this == qs);
+}
+
+bool QuickString::operator < (const QuickString &qs) const {
+ return (memcmp(_buffer, qs._buffer, max(_currSize, qs._currSize)) < 0);
+}
+
+bool QuickString::operator > (const QuickString &qs) const {
+ return (memcmp(_buffer, qs._buffer, max(_currSize, qs._currSize))> 0);
+}
+
+void QuickString::set(const char *inBuf, size_t newLen) {
+ reserve(newLen);
+ clear();
+ memcpy(_buffer, inBuf, newLen);
+ _currSize = newLen;
+}
+
+void QuickString::reserve(size_t newLen) {
+ newLen++; //always leave room for a null termninator.
+ if (_currCapacity <= newLen) {
+ while (_currCapacity <= newLen) {
+ _currCapacity = _currCapacity << 1;
+ }
+ _buffer = (char *)realloc(_buffer, _currCapacity );
+ if (_buffer == NULL) {
+ fprintf(stderr, "Error: failed to reallocate string.\n");
+ _currSize = 0;
+ _currCapacity = 0;
+ exit(1);
+ }
+ //initialize newly reserved memory.
+ memset(_buffer + _currSize, 0, _currCapacity - _currSize);
+ }
+}
+
+void QuickString::append(char c)
+{
+ reserve(_currSize +1);
+ _buffer[_currSize] = c;
+ _currSize++;
+}
+
+void QuickString::append(const char *inBuf, size_t inBufLen)
+{
+ reserve(_currSize + inBufLen);
+ memcpy(_buffer + _currSize, inBuf, inBufLen);
+ _currSize += inBufLen;
+}
+
+void QuickString::append(int num) {
+ int2str(num, *this, true);
+}
+QuickString &QuickString::assign(const char *inBuf, size_t inBufLen)
+{
+ clear();
+ append(inBuf, inBufLen);
+ return *this;
+}
+
+void QuickString::resize(size_t newSize, char fillChar)
+{
+ if (newSize > _currSize) { //grow the string, pad with fillChar
+ reserve(newSize);
+ memset(_buffer + _currSize, fillChar, newSize -_currSize);
+ } else if (newSize < _currSize) { //cut off characters from the end
+ memset(_buffer + newSize, 0, _currSize - newSize);
+ }
+ _currSize = newSize;
+}
+
+
+void QuickString::substr (QuickString &newStr, size_t pos, size_t len) const
+{
+ if (pos >= _currSize) {
+ return;
+ }
+ if (pos + len >= _currSize) {
+ len = _currSize - pos;
+ }
+ newStr.set(_buffer + pos, len);
+}
+
+ostream &operator << (ostream &out, const QuickString &str) {
+ out << str._buffer;
+ return out;
+}
diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
new file mode 100644
index 0000000..5fdc0fc
--- /dev/null
+++ b/src/utils/general/QuickString.h
@@ -0,0 +1,72 @@
+/*
+ * QuickString.h
+ *
+ * Created on: Dec 3, 2012
+ * Author: nek3d
+ */
+
+#ifndef QUICKSTRING_H_
+#define QUICKSTRING_H_
+
+using namespace std;
+#include <string>
+#include <climits>
+#include <ostream>
+
+class QuickString {
+public:
+ QuickString(size_t capacity = DEFAULT_CAPACITY);
+ QuickString(const QuickString &); //need explicit copy constructor
+ //so address of _buffer member is not copied! Each QuickString object
+ //needs to build it's own buffer.
+ QuickString(const char *);
+ QuickString(const string &);
+ QuickString(char c);
+ ~QuickString();
+ size_t size() const { return _currSize; }
+ size_t capacity() const { return _currCapacity; }
+ void reserve(size_t newCapacity=0);
+ bool empty() const { return _currSize == 0; }
+
+ void clear(); //only clears buffer, doesn't delete it.
+ QuickString &operator = (const string &);
+ QuickString &operator = (const char *);
+ QuickString &operator = (const QuickString &);
+ QuickString &operator += (const QuickString &);
+ QuickString &operator += (const string &);
+ QuickString &operator += (const char *);
+ QuickString &operator += (char);
+
+ friend ostream &operator << (ostream &out, const QuickString &str);
+ bool operator == (const QuickString &) const;
+ bool operator == (const string &) const;
+ bool operator == (const char *) const;
+ bool operator != (const QuickString &) const;
+ bool operator < (const QuickString &) const;
+ bool operator > (const QuickString &) const;
+ const char *c_str() const { return _buffer; }
+ const string str() const { return _buffer; }
+ const char &operator [] (int pos) const { return _buffer[pos]; }
+ char &operator [] (int pos) { return _buffer[pos]; }
+
+ void append(const QuickString &str) { append(str.c_str(), str.size()); }
+ void append(const char *buf, size_t bufLen);
+ void append(char c);
+ void append(int num);
+
+ QuickString &assign(const char *str, size_t n);
+ void resize(size_t n, char c = '\0');
+ void substr(QuickString &newStr, size_t pos = 0, size_t len = UINT_MAX) const;
+
+private:
+ char *_buffer;
+ size_t _currCapacity;
+ size_t _currSize;
+
+ static const int DEFAULT_CAPACITY = 8;
+ void build();
+ void set(const char *len, size_t size);
+};
+
+
+#endif /* QUICKSTRING_H_ */
diff --git a/src/utils/genomeFile/Makefile b/src/utils/genomeFile/Makefile
deleted file mode 100644
index 680343c..0000000
--- a/src/utils/genomeFile/Makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-OBJ_DIR = ../../../obj/
-BIN_DIR = ../../../bin/
-UTILITIES_DIR = ../
-# -------------------
-# define our includes
-# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/ \
- -I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/BamTools/include/
-
-# ----------------------------------
-# define our source and object files
-# ----------------------------------
-SOURCES= genomeFile.cpp genomeFile.h
-OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=lineFileUtilities.o fileType.o
-EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
-BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-
-$(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-
-$(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/fileType/
-
-clean:
- @echo "Cleaning up."
- @rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
-
-.PHONY: clean
diff --git a/src/utils/tabFile/tabFile.cpp b/src/utils/tabFile/tabFile.cpp
index e226a06..4ea3912 100644
--- a/src/utils/tabFile/tabFile.cpp
+++ b/src/utils/tabFile/tabFile.cpp
@@ -36,8 +36,14 @@ void TabFile::Open(void) {
delete _tabStream;
_tabStream = new igzstream(_tabFile.c_str(), ios::in);
}
- if ( !(_tabStream->good()) ) {
- cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
+ if ( _tabStream->fail() ) {
+ cerr << "Error: The requested file ("
+ << _tabFile
+ << ") "
+ << "could not be opened. "
+ << "Error message: ("
+ << strerror(errno)
+ << "). Exiting!" << endl;
exit (1);
}
}
@@ -60,6 +66,11 @@ TabLineStatus TabFile::GetNextTabLine(TAB_FIELDS &tabFields, int &lineNum) {
// parse the tabStream pointer
getline(*_tabStream, tabLine);
+
+ if (tabLine[tabLine.size()-1] == '\r') {
+ tabLine.resize(tabLine.size()-1);
+ }
+
lineNum++;
// split into a string vector.
diff --git a/src/utils/version/version_release.txt b/src/utils/version/version_release.txt
index a228e67..a95b4ba 100644
--- a/src/utils/version/version_release.txt
+++ b/src/utils/version/version_release.txt
@@ -1,5 +1,5 @@
-# This file was auto-generated by running "make setversion VERSION=v2.17.0"
-# on Sat Nov 3 16:11:06 EDT 2012 .
+# This file was auto-generated by running "make setversion VERSION=v2.19.0"
+# on Sat Feb 8 21:29:06 EST 2014 .
# Please do not edit or commit this file manually.
#
-v2.17.0
+v2.19.0
diff --git a/src/windowBed/windowMain.cpp b/src/windowBed/windowMain.cpp
index 4fd6048..766a281 100644
--- a/src/windowBed/windowMain.cpp
+++ b/src/windowBed/windowMain.cpp
@@ -216,7 +216,7 @@ void window_help(void) {
cerr << "Options: " << endl;
- cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
+ cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well. Replaces -a." << endl << endl;
cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl;
diff --git a/src/windowMaker/Makefile b/src/windowMaker/Makefile
index b51e487..35c6ca3 100644
--- a/src/windowMaker/Makefile
+++ b/src/windowMaker/Makefile
@@ -5,7 +5,7 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/genomeFile/ \
+INCLUDES = -I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/bedFile/ \
-I$(UTILITIES_DIR)/gzstream/ \
-I$(UTILITIES_DIR)/fileType/ \
diff --git a/src/windowMaker/windowMaker.h b/src/windowMaker/windowMaker.h
index b06b46e..3c7d14f 100644
--- a/src/windowMaker/windowMaker.h
+++ b/src/windowMaker/windowMaker.h
@@ -9,7 +9,7 @@ aaronquinlan at gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
-#include "genomeFile.h"
+#include "GenomeFile.h"
#include "bedFile.h"
using namespace std;
diff --git a/test/bamtobed/test-bamtobed.sh b/test/bamtobed/test-bamtobed.sh
index 0d028e7..193a3c1 100644
--- a/test/bamtobed/test-bamtobed.sh
+++ b/test/bamtobed/test-bamtobed.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -18,6 +18,7 @@ samtools view -Sb one_block.sam > one_block.bam 2>/dev/null
samtools view -Sb two_blocks.sam > two_blocks.bam 2>/dev/null
samtools view -Sb three_blocks.sam > three_blocks.bam 2>/dev/null
samtools view -Sb sam-w-del.sam > sam-w-del.bam 2>/dev/null
+samtools view -Sb two_blocks_w_D.sam > two_blocks_w_D.bam 2>/dev/null
##################################################################
@@ -110,4 +111,66 @@ $BT bamtobed -i three_blocks.bam -bed12 | $BT bed12tobed6 > bed12
check split bed12
rm split bed12
+##################################################################
+# Test an alignment with a D operator and N operator -split option
+##################################################################
+echo " bamtobed.t9...\c"
+echo \
+"chr1 0 15 two_blocks_1_1/2 40 +
+chr1 25 40 two_blocks_1_1/2 40 +
+chr1 99 129 two_blocks_1_2/1 40 +
+chr1 0 15 two_blocks_2_1/2 40 +
+chr1 25 42 two_blocks_2_1/2 40 +
+chr1 99 129 two_blocks_2_2/1 40 +" > exp
+$BT bamtobed -i two_blocks_w_D.bam -split > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -splitD option
+##################################################################
+echo " bamtobed.t10...\c"
+echo \
+"chr1 0 15 two_blocks_1_1/2 40 +
+chr1 25 40 two_blocks_1_1/2 40 +
+chr1 99 129 two_blocks_1_2/1 40 +
+chr1 0 15 two_blocks_2_1/2 40 +
+chr1 25 35 two_blocks_2_1/2 40 +
+chr1 37 42 two_blocks_2_1/2 40 +
+chr1 99 129 two_blocks_2_2/1 40 +" > exp
+$BT bamtobed -i two_blocks_w_D.bam -splitD > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -bed12 option
+##################################################################
+echo " bamtobed.t9...\c"
+echo \
+"chr1 0 40 two_blocks_1_1/2 40 + 0 40 255,0,0 2 15,15 0,25
+chr1 99 129 two_blocks_1_2/1 40 + 99 129 255,0,0 1 30 0
+chr1 0 42 two_blocks_2_1/2 40 + 0 42 255,0,0 2 15,17 0,25
+chr1 99 129 two_blocks_2_2/1 40 + 99 129 255,0,0 1 30 0" > exp
+$BT bamtobed -i two_blocks_w_D.bam -bed12 > obs
+check exp obs
+rm exp obs
+
+
+##################################################################
+# Test an alignment with a D operator and N operator -bed12 option
+##################################################################
+echo " bamtobed.t11...\c"
+echo \
+"chr1 0 40 two_blocks_1_1/2 40 + 0 40 255,0,0 2 15,15 0,25
+chr1 99 129 two_blocks_1_2/1 40 + 99 129 255,0,0 1 30 0
+chr1 0 42 two_blocks_2_1/2 40 + 0 42 255,0,0 3 15,10,5 0,25,37
+chr1 99 129 two_blocks_2_2/1 40 + 99 129 255,0,0 1 30 0" > exp
+$BT bamtobed -i two_blocks_w_D.bam -bed12 -splitD > obs
+
+check exp obs
+rm exp obs
+
+
rm *.bam
diff --git a/test/bamtobed/two_blocks_w_D.sam b/test/bamtobed/two_blocks_w_D.sam
new file mode 100644
index 0000000..00ddff2
--- /dev/null
+++ b/test/bamtobed/two_blocks_w_D.sam
@@ -0,0 +1,6 @@
+ at HD VN:1.0 GO:none SO:coordinate
+ at SQ SN:chr1 LN:249250621
+two_blocks_1_1 163 chr1 1 40 15M10N15M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_1_2 99 chr1 100 40 30M * 0 0 AGGCGATGCTAACGAAAAATTCGGAAATTT CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_2_1 163 chr1 1 40 15M10N10M2D5M * 0 0 GAAGGCCACCGCCGCGGTTATTTTCCTTCA CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
+two_blocks_2_2 99 chr1 100 40 30M * 0 0 AGGCGATGCTAACGAAAAATTCGGAAATTT CCCDDB?=FJIIJIGFJIJHIJJJJJJJJI MD:Z:50 XA:i:2
diff --git a/test/bed12tobed6/test-bed12tobed6.sh b/test/bed12tobed6/test-bed12tobed6.sh
index 1cc53e8..ae7757b 100644
--- a/test/bed12tobed6/test-bed12tobed6.sh
+++ b/test/bed12tobed6/test-bed12tobed6.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/closest/close-a.bed b/test/closest/close-a.bed
new file mode 100644
index 0000000..ad2095e
--- /dev/null
+++ b/test/closest/close-a.bed
@@ -0,0 +1,8 @@
+track name="Test Bed" maxheightpixels=120:120
+chr1 100 101
+chr1 200 201
+chr1 300 301
+chr1 100000 100010
+chr1 100020 100040
+chr2 1 10
+chr2 20 30
diff --git a/test/closest/close-b.bed b/test/closest/close-b.bed
new file mode 100644
index 0000000..65b4e00
--- /dev/null
+++ b/test/closest/close-b.bed
@@ -0,0 +1,7 @@
+track name="Test Bed 2" maxheightpixels=120:120
+chr1 100 101
+chr1 150 201
+chr1 175 375
+chr3 20 30
+chr7 55209979 55210130
+chr7 55210220 55210688
diff --git a/test/closest/strand-test-a.bed b/test/closest/strand-test-a.bed
new file mode 100644
index 0000000..3d31b62
--- /dev/null
+++ b/test/closest/strand-test-a.bed
@@ -0,0 +1,2 @@
+chr1 100 200 a 10 +
+
diff --git a/test/closest/strand-test-b.bed b/test/closest/strand-test-b.bed
new file mode 100644
index 0000000..1957ceb
--- /dev/null
+++ b/test/closest/strand-test-b.bed
@@ -0,0 +1,3 @@
+chr1 90 120 b 1 -
+
+
diff --git a/test/closest/test-closest.sh b/test/closest/test-closest.sh
index e2d50d7..7a0ded2 100644
--- a/test/closest/test-closest.sh
+++ b/test/closest/test-closest.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -81,3 +81,89 @@ chr1 55 58 break2 chr1 40 50 break1 6" > exp
$BT closest -a a.names.bed -b b.names.bed -d -N > obs
check obs exp
rm obs exp
+
+###########################################################
+# test closest forcing -s yet no matching strands on chrom
+###########################################################
+echo " closest.t7...\c"
+echo \
+"chr1 100 200 a 10 + . -1 -1 . -1 ." > exp
+$BT closest -a strand-test-a.bed -b strand-test-b.bed -s > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test closest forcing -S with only an opp strands on chrom
+###########################################################
+echo " closest.t8...\c"
+echo \
+"chr1 100 200 a 10 + chr1 90 120 b 1 -" > exp
+$BT closest -a strand-test-a.bed -b strand-test-b.bed -S > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# test reproting of all overlapping features
+###########################################################
+echo " closest.t9...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 150 201
+chr1 200 201 chr1 175 375
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of first overlapping feature
+###########################################################
+echo " closest.t10...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 150 201
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -t first > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of last overlapping feature
+###########################################################
+echo " closest.t11...\c"
+echo \
+"chr1 100 101 chr1 100 101
+chr1 200 201 chr1 175 375
+chr1 300 301 chr1 175 375
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -t last > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test reproting of no overlapping feature
+###########################################################
+echo " closest.t12...\c"
+echo \
+"chr1 100 101 chr1 150 201
+chr1 200 201 chr1 100 101
+chr1 300 301 chr1 150 201
+chr1 100000 100010 chr1 175 375
+chr1 100020 100040 chr1 175 375
+chr2 1 10 . -1 -1
+chr2 20 30 . -1 -1" > exp
+$BT closest -a close-a.bed -b close-b.bed -io > obs
+check obs exp
+rm obs exp
diff --git a/test/cluster/test-cluster.sh b/test/cluster/test-cluster.sh
index b8e5a62..07c425b 100644
--- a/test/cluster/test-cluster.sh
+++ b/test/cluster/test-cluster.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/coverage/test-coverage.sh b/test/coverage/test-coverage.sh
index 969e1c1..4c43bd4 100644
--- a/test/coverage/test-coverage.sh
+++ b/test/coverage/test-coverage.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/expand/test-expand.sh b/test/expand/test-expand.sh
index a8c1183..26ac22e 100644
--- a/test/expand/test-expand.sh
+++ b/test/expand/test-expand.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/flank/test-flank.sh b/test/flank/test-flank.sh
index c9c6855..2101fd7 100644
--- a/test/flank/test-flank.sh
+++ b/test/flank/test-flank.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/general/empty.bed b/test/general/empty.bed
new file mode 100644
index 0000000..e69de29
diff --git a/test/general/non-empty.bed.gz b/test/general/non-empty.bed.gz
new file mode 100644
index 0000000..e508bd9
Binary files /dev/null and b/test/general/non-empty.bed.gz differ
diff --git a/test/general/test-general.sh b/test/general/test-general.sh
index e1e9ef2..6028bf1 100644
--- a/test/general/test-general.sh
+++ b/test/general/test-general.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -65,3 +65,34 @@ echo "It looks as though you have less than 3 columns at line: 1. Are you sure
check obs exp
rm obs exp
+
+###########################################################
+# Fail on non-existent files.
+###########################################################
+echo " general.t06...\c"
+$BT merge -i idontexist.bed 2> obs
+echo "Error: The requested file (idontexist.bed) could not be opened. Error message: (No such file or directory). Exiting!" > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Don't fail on existent, yet empty files.
+###########################################################
+echo " general.t07...\c"
+$BT merge -i empty.bed > obs
+touch exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Process gzipped files.
+###########################################################
+echo " general.t08...\c"
+$BT merge -i non-empty.bed.gz > obs
+echo "chr1 10 21" > exp
+check obs exp
+rm obs exp
+
+
diff --git a/test/genomecov/test-genomecov.sh b/test/genomecov/test-genomecov.sh
index b7102d5..2c00c24 100644
--- a/test/genomecov/test-genomecov.sh
+++ b/test/genomecov/test-genomecov.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/getfasta/t_fH.fa b/test/getfasta/t_fH.fa
new file mode 100644
index 0000000..d58c3d7
--- /dev/null
+++ b/test/getfasta/t_fH.fa
@@ -0,0 +1,6 @@
+>chr1 assembled by consortium X
+aggggggggg
+cggggggggg
+tggggggggg
+aggggggggg
+cggggggggg
diff --git a/test/getfasta/t_fH.fa.fai b/test/getfasta/t_fH.fa.fai
new file mode 100644
index 0000000..924e70d
--- /dev/null
+++ b/test/getfasta/t_fH.fa.fai
@@ -0,0 +1 @@
+chr1 assembled by consortium X 50 32 10 11
diff --git a/test/getfasta/test-getfasta.sh b/test/getfasta/test-getfasta.sh
index 64dbcd5..0e7774d 100644
--- a/test/getfasta/test-getfasta.sh
+++ b/test/getfasta/test-getfasta.sh
@@ -6,17 +6,19 @@
# aggggggggg
# cggggggggg
+BT=${BT-../../bin/bedtools}
+
check()
{
- if $1 = $2; then
- echo ok
- else
- echo fail
- fi
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
}
echo " getfasta.t01...\c"
-LINES=$(echo $'chr1\t1\t10' | ../../bin/bedtools getfasta -fi t.fa -bed stdin -fo - | awk 'END{ print NR }')
+LINES=$(echo $'chr1\t1\t10' | $BT getfasta -fi t.fa -bed stdin -fo - | awk 'END{ print NR }')
if [ "$LINES" != "2" ]; then
echo fail
else
@@ -24,7 +26,7 @@ else
fi
echo " getfasta.t02...\c"
-LEN=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 2){ print length($0) }')
+LEN=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 2){ print length($0) }')
if [ "$LINES" != "2" ]; then
echo fail
else
@@ -32,7 +34,7 @@ else
fi
echo " getfasta.t03...\c"
-SEQ=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 4){ print $0 }')
+SEQ=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "cta" ]; then
echo fail
else
@@ -41,7 +43,7 @@ fi
# test -fo -
echo " getfasta.t04...\c"
-SEQ=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
+SEQ=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "cta" ]; then
echo fail
else
@@ -51,9 +53,27 @@ fi
# test -split with -s -
echo " getfasta.t05...\c"
-SEQ=$(../../bin/bedtools getfasta -split -s -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
+SEQ=$($BT getfasta -split -s -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "tag" ]; then
echo fail
else
echo ok
-fi
\ No newline at end of file
+fi
+
+# test -fullHeader
+echo " getfasta.t06...\c"
+LINES=$(echo $'chr1 assembled by consortium X\t1\t10' | $BT getfasta -fullHeader -fi t_fH.fa -bed stdin -fo - | awk 'END{ print NR }')
+if [ "$LINES" != "2" ]; then
+ echo fail
+else
+ echo ok
+fi
+
+# test without -fullHeader
+echo " getfasta.t07...\c"
+echo "WARNING. chromosome (chr1 assembled by consortium X) was not found in the FASTA file. Skipping." > exp
+echo $'chr1 assembled by consortium X\t1\t10' | $BT getfasta -fi t_fH.fa -bed - -fo - 2> obs
+
+check obs exp
+
+rm obs exp
\ No newline at end of file
diff --git a/test/groupBy/test-groupby.sh b/test/groupBy/test-groupby.sh
index f95782a..a20f7cc 100644
--- a/test/groupBy/test-groupby.sh
+++ b/test/groupBy/test-groupby.sh
@@ -1,7 +1,9 @@
-lines_a=$(../../bin/groupBy -g 3-1 -o collapse -c 4 -i ../map/values3.bed | wc -l)
-lines_b=$(../../bin/groupBy -g 1-3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
-lines_c=$(../../bin/groupBy -g 1,2,3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
-lines_d=$(../../bin/groupBy -g 1-2,3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
+BT=${BT-../../bin/bedtools}
+
+lines_a=$($BT groupby -g 3-1 -o collapse -c 4 -i ../map/values3.bed | wc -l)
+lines_b=$($BT groupby -g 1-3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
+lines_c=$($BT groupby -g 1,2,3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
+lines_d=$($BT groupby -g 1-2,3 -o collapse -c 4 -i ../map/values3.bed | wc -l)
check(){
if [ "$1" != "$2" ]; then
@@ -15,13 +17,13 @@ check $lines_a $lines_d
H=$(head -n 1 values3.header.bed)
-A=$(../../bin/bedtools groupby -i values3.header.bed -g 1,2,3 -c 4 -o concat -inheader | head -n 1)
+A=$($BT groupby -i values3.header.bed -g 1,2,3 -c 4 -o concat -inheader | head -n 1)
if [ "$A" != $'chr1\t0\t10\ta1' ]; then
echo "fail groupby"
fi
-B=$(../../bin/bedtools groupby -i values3.header.bed -g 1,2,3 -c 4 -o concat -header | head -n 1)
+B=$($BT groupby -i values3.header.bed -g 1,2,3 -c 4 -o concat -header | head -n 1)
if [ "$B" != $'#chrom\tstart\tend\tconcat(A)' ]; then
echo "fail groupby"
diff --git a/test/intersect/a.bam b/test/intersect/a.bam
new file mode 100644
index 0000000..f56cccf
Binary files /dev/null and b/test/intersect/a.bam differ
diff --git a/test/intersect/aVSb.bam b/test/intersect/aVSb.bam
new file mode 100644
index 0000000..911fa82
Binary files /dev/null and b/test/intersect/aVSb.bam differ
diff --git a/test/intersect/aWithHeaderVsB.txt b/test/intersect/aWithHeaderVsB.txt
new file mode 100644
index 0000000..0d5223a
--- /dev/null
+++ b/test/intersect/aWithHeaderVsB.txt
@@ -0,0 +1,4002 @@
+# This is line 0 of a file with a large header.
+# This is line 1 of a file with a large header.
+# This is line 2 of a file with a large header.
+# This is line 3 of a file with a large header.
+# This is line 4 of a file with a large header.
+# This is line 5 of a file with a large header.
+# This is line 6 of a file with a large header.
+# This is line 7 of a file with a large header.
+# This is line 8 of a file with a large header.
+# This is line 9 of a file with a large header.
+# This is line 10 of a file with a large header.
+# This is line 11 of a file with a large header.
+# This is line 12 of a file with a large header.
+# This is line 13 of a file with a large header.
+# This is line 14 of a file with a large header.
+# This is line 15 of a file with a large header.
+# This is line 16 of a file with a large header.
+# This is line 17 of a file with a large header.
+# This is line 18 of a file with a large header.
+# This is line 19 of a file with a large header.
+# This is line 20 of a file with a large header.
+# This is line 21 of a file with a large header.
+# This is line 22 of a file with a large header.
+# This is line 23 of a file with a large header.
+# This is line 24 of a file with a large header.
+# This is line 25 of a file with a large header.
+# This is line 26 of a file with a large header.
+# This is line 27 of a file with a large header.
+# This is line 28 of a file with a large header.
+# This is line 29 of a file with a large header.
+# This is line 30 of a file with a large header.
+# This is line 31 of a file with a large header.
+# This is line 32 of a file with a large header.
+# This is line 33 of a file with a large header.
+# This is line 34 of a file with a large header.
+# This is line 35 of a file with a large header.
+# This is line 36 of a file with a large header.
+# This is line 37 of a file with a large header.
+# This is line 38 of a file with a large header.
+# This is line 39 of a file with a large header.
+# This is line 40 of a file with a large header.
+# This is line 41 of a file with a large header.
+# This is line 42 of a file with a large header.
+# This is line 43 of a file with a large header.
+# This is line 44 of a file with a large header.
+# This is line 45 of a file with a large header.
+# This is line 46 of a file with a large header.
+# This is line 47 of a file with a large header.
+# This is line 48 of a file with a large header.
+# This is line 49 of a file with a large header.
+# This is line 50 of a file with a large header.
+# This is line 51 of a file with a large header.
+# This is line 52 of a file with a large header.
+# This is line 53 of a file with a large header.
+# This is line 54 of a file with a large header.
+# This is line 55 of a file with a large header.
+# This is line 56 of a file with a large header.
+# This is line 57 of a file with a large header.
+# This is line 58 of a file with a large header.
+# This is line 59 of a file with a large header.
+# This is line 60 of a file with a large header.
+# This is line 61 of a file with a large header.
+# This is line 62 of a file with a large header.
+# This is line 63 of a file with a large header.
+# This is line 64 of a file with a large header.
+# This is line 65 of a file with a large header.
+# This is line 66 of a file with a large header.
+# This is line 67 of a file with a large header.
+# This is line 68 of a file with a large header.
+# This is line 69 of a file with a large header.
+# This is line 70 of a file with a large header.
+# This is line 71 of a file with a large header.
+# This is line 72 of a file with a large header.
+# This is line 73 of a file with a large header.
+# This is line 74 of a file with a large header.
+# This is line 75 of a file with a large header.
+# This is line 76 of a file with a large header.
+# This is line 77 of a file with a large header.
+# This is line 78 of a file with a large header.
+# This is line 79 of a file with a large header.
+# This is line 80 of a file with a large header.
+# This is line 81 of a file with a large header.
+# This is line 82 of a file with a large header.
+# This is line 83 of a file with a large header.
+# This is line 84 of a file with a large header.
+# This is line 85 of a file with a large header.
+# This is line 86 of a file with a large header.
+# This is line 87 of a file with a large header.
+# This is line 88 of a file with a large header.
+# This is line 89 of a file with a large header.
+# This is line 90 of a file with a large header.
+# This is line 91 of a file with a large header.
+# This is line 92 of a file with a large header.
+# This is line 93 of a file with a large header.
+# This is line 94 of a file with a large header.
+# This is line 95 of a file with a large header.
+# This is line 96 of a file with a large header.
+# This is line 97 of a file with a large header.
+# This is line 98 of a file with a large header.
+# This is line 99 of a file with a large header.
+# This is line 100 of a file with a large header.
+# This is line 101 of a file with a large header.
+# This is line 102 of a file with a large header.
+# This is line 103 of a file with a large header.
+# This is line 104 of a file with a large header.
+# This is line 105 of a file with a large header.
+# This is line 106 of a file with a large header.
+# This is line 107 of a file with a large header.
+# This is line 108 of a file with a large header.
+# This is line 109 of a file with a large header.
+# This is line 110 of a file with a large header.
+# This is line 111 of a file with a large header.
+# This is line 112 of a file with a large header.
+# This is line 113 of a file with a large header.
+# This is line 114 of a file with a large header.
+# This is line 115 of a file with a large header.
+# This is line 116 of a file with a large header.
+# This is line 117 of a file with a large header.
+# This is line 118 of a file with a large header.
+# This is line 119 of a file with a large header.
+# This is line 120 of a file with a large header.
+# This is line 121 of a file with a large header.
+# This is line 122 of a file with a large header.
+# This is line 123 of a file with a large header.
+# This is line 124 of a file with a large header.
+# This is line 125 of a file with a large header.
+# This is line 126 of a file with a large header.
+# This is line 127 of a file with a large header.
+# This is line 128 of a file with a large header.
+# This is line 129 of a file with a large header.
+# This is line 130 of a file with a large header.
+# This is line 131 of a file with a large header.
+# This is line 132 of a file with a large header.
+# This is line 133 of a file with a large header.
+# This is line 134 of a file with a large header.
+# This is line 135 of a file with a large header.
+# This is line 136 of a file with a large header.
+# This is line 137 of a file with a large header.
+# This is line 138 of a file with a large header.
+# This is line 139 of a file with a large header.
+# This is line 140 of a file with a large header.
+# This is line 141 of a file with a large header.
+# This is line 142 of a file with a large header.
+# This is line 143 of a file with a large header.
+# This is line 144 of a file with a large header.
+# This is line 145 of a file with a large header.
+# This is line 146 of a file with a large header.
+# This is line 147 of a file with a large header.
+# This is line 148 of a file with a large header.
+# This is line 149 of a file with a large header.
+# This is line 150 of a file with a large header.
+# This is line 151 of a file with a large header.
+# This is line 152 of a file with a large header.
+# This is line 153 of a file with a large header.
+# This is line 154 of a file with a large header.
+# This is line 155 of a file with a large header.
+# This is line 156 of a file with a large header.
+# This is line 157 of a file with a large header.
+# This is line 158 of a file with a large header.
+# This is line 159 of a file with a large header.
+# This is line 160 of a file with a large header.
+# This is line 161 of a file with a large header.
+# This is line 162 of a file with a large header.
+# This is line 163 of a file with a large header.
+# This is line 164 of a file with a large header.
+# This is line 165 of a file with a large header.
+# This is line 166 of a file with a large header.
+# This is line 167 of a file with a large header.
+# This is line 168 of a file with a large header.
+# This is line 169 of a file with a large header.
+# This is line 170 of a file with a large header.
+# This is line 171 of a file with a large header.
+# This is line 172 of a file with a large header.
+# This is line 173 of a file with a large header.
+# This is line 174 of a file with a large header.
+# This is line 175 of a file with a large header.
+# This is line 176 of a file with a large header.
+# This is line 177 of a file with a large header.
+# This is line 178 of a file with a large header.
+# This is line 179 of a file with a large header.
+# This is line 180 of a file with a large header.
+# This is line 181 of a file with a large header.
+# This is line 182 of a file with a large header.
+# This is line 183 of a file with a large header.
+# This is line 184 of a file with a large header.
+# This is line 185 of a file with a large header.
+# This is line 186 of a file with a large header.
+# This is line 187 of a file with a large header.
+# This is line 188 of a file with a large header.
+# This is line 189 of a file with a large header.
+# This is line 190 of a file with a large header.
+# This is line 191 of a file with a large header.
+# This is line 192 of a file with a large header.
+# This is line 193 of a file with a large header.
+# This is line 194 of a file with a large header.
+# This is line 195 of a file with a large header.
+# This is line 196 of a file with a large header.
+# This is line 197 of a file with a large header.
+# This is line 198 of a file with a large header.
+# This is line 199 of a file with a large header.
+# This is line 200 of a file with a large header.
+# This is line 201 of a file with a large header.
+# This is line 202 of a file with a large header.
+# This is line 203 of a file with a large header.
+# This is line 204 of a file with a large header.
+# This is line 205 of a file with a large header.
+# This is line 206 of a file with a large header.
+# This is line 207 of a file with a large header.
+# This is line 208 of a file with a large header.
+# This is line 209 of a file with a large header.
+# This is line 210 of a file with a large header.
+# This is line 211 of a file with a large header.
+# This is line 212 of a file with a large header.
+# This is line 213 of a file with a large header.
+# This is line 214 of a file with a large header.
+# This is line 215 of a file with a large header.
+# This is line 216 of a file with a large header.
+# This is line 217 of a file with a large header.
+# This is line 218 of a file with a large header.
+# This is line 219 of a file with a large header.
+# This is line 220 of a file with a large header.
+# This is line 221 of a file with a large header.
+# This is line 222 of a file with a large header.
+# This is line 223 of a file with a large header.
+# This is line 224 of a file with a large header.
+# This is line 225 of a file with a large header.
+# This is line 226 of a file with a large header.
+# This is line 227 of a file with a large header.
+# This is line 228 of a file with a large header.
+# This is line 229 of a file with a large header.
+# This is line 230 of a file with a large header.
+# This is line 231 of a file with a large header.
+# This is line 232 of a file with a large header.
+# This is line 233 of a file with a large header.
+# This is line 234 of a file with a large header.
+# This is line 235 of a file with a large header.
+# This is line 236 of a file with a large header.
+# This is line 237 of a file with a large header.
+# This is line 238 of a file with a large header.
+# This is line 239 of a file with a large header.
+# This is line 240 of a file with a large header.
+# This is line 241 of a file with a large header.
+# This is line 242 of a file with a large header.
+# This is line 243 of a file with a large header.
+# This is line 244 of a file with a large header.
+# This is line 245 of a file with a large header.
+# This is line 246 of a file with a large header.
+# This is line 247 of a file with a large header.
+# This is line 248 of a file with a large header.
+# This is line 249 of a file with a large header.
+# This is line 250 of a file with a large header.
+# This is line 251 of a file with a large header.
+# This is line 252 of a file with a large header.
+# This is line 253 of a file with a large header.
+# This is line 254 of a file with a large header.
+# This is line 255 of a file with a large header.
+# This is line 256 of a file with a large header.
+# This is line 257 of a file with a large header.
+# This is line 258 of a file with a large header.
+# This is line 259 of a file with a large header.
+# This is line 260 of a file with a large header.
+# This is line 261 of a file with a large header.
+# This is line 262 of a file with a large header.
+# This is line 263 of a file with a large header.
+# This is line 264 of a file with a large header.
+# This is line 265 of a file with a large header.
+# This is line 266 of a file with a large header.
+# This is line 267 of a file with a large header.
+# This is line 268 of a file with a large header.
+# This is line 269 of a file with a large header.
+# This is line 270 of a file with a large header.
+# This is line 271 of a file with a large header.
+# This is line 272 of a file with a large header.
+# This is line 273 of a file with a large header.
+# This is line 274 of a file with a large header.
+# This is line 275 of a file with a large header.
+# This is line 276 of a file with a large header.
+# This is line 277 of a file with a large header.
+# This is line 278 of a file with a large header.
+# This is line 279 of a file with a large header.
+# This is line 280 of a file with a large header.
+# This is line 281 of a file with a large header.
+# This is line 282 of a file with a large header.
+# This is line 283 of a file with a large header.
+# This is line 284 of a file with a large header.
+# This is line 285 of a file with a large header.
+# This is line 286 of a file with a large header.
+# This is line 287 of a file with a large header.
+# This is line 288 of a file with a large header.
+# This is line 289 of a file with a large header.
+# This is line 290 of a file with a large header.
+# This is line 291 of a file with a large header.
+# This is line 292 of a file with a large header.
+# This is line 293 of a file with a large header.
+# This is line 294 of a file with a large header.
+# This is line 295 of a file with a large header.
+# This is line 296 of a file with a large header.
+# This is line 297 of a file with a large header.
+# This is line 298 of a file with a large header.
+# This is line 299 of a file with a large header.
+# This is line 300 of a file with a large header.
+# This is line 301 of a file with a large header.
+# This is line 302 of a file with a large header.
+# This is line 303 of a file with a large header.
+# This is line 304 of a file with a large header.
+# This is line 305 of a file with a large header.
+# This is line 306 of a file with a large header.
+# This is line 307 of a file with a large header.
+# This is line 308 of a file with a large header.
+# This is line 309 of a file with a large header.
+# This is line 310 of a file with a large header.
+# This is line 311 of a file with a large header.
+# This is line 312 of a file with a large header.
+# This is line 313 of a file with a large header.
+# This is line 314 of a file with a large header.
+# This is line 315 of a file with a large header.
+# This is line 316 of a file with a large header.
+# This is line 317 of a file with a large header.
+# This is line 318 of a file with a large header.
+# This is line 319 of a file with a large header.
+# This is line 320 of a file with a large header.
+# This is line 321 of a file with a large header.
+# This is line 322 of a file with a large header.
+# This is line 323 of a file with a large header.
+# This is line 324 of a file with a large header.
+# This is line 325 of a file with a large header.
+# This is line 326 of a file with a large header.
+# This is line 327 of a file with a large header.
+# This is line 328 of a file with a large header.
+# This is line 329 of a file with a large header.
+# This is line 330 of a file with a large header.
+# This is line 331 of a file with a large header.
+# This is line 332 of a file with a large header.
+# This is line 333 of a file with a large header.
+# This is line 334 of a file with a large header.
+# This is line 335 of a file with a large header.
+# This is line 336 of a file with a large header.
+# This is line 337 of a file with a large header.
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+# This is line 339 of a file with a large header.
+# This is line 340 of a file with a large header.
+# This is line 341 of a file with a large header.
+# This is line 342 of a file with a large header.
+# This is line 343 of a file with a large header.
+# This is line 344 of a file with a large header.
+# This is line 345 of a file with a large header.
+# This is line 346 of a file with a large header.
+# This is line 347 of a file with a large header.
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+# This is line 351 of a file with a large header.
+# This is line 352 of a file with a large header.
+# This is line 353 of a file with a large header.
+# This is line 354 of a file with a large header.
+# This is line 355 of a file with a large header.
+# This is line 356 of a file with a large header.
+# This is line 357 of a file with a large header.
+# This is line 358 of a file with a large header.
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+# This is line 360 of a file with a large header.
+# This is line 361 of a file with a large header.
+# This is line 362 of a file with a large header.
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+# This is line 365 of a file with a large header.
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+# This is line 367 of a file with a large header.
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+# This is line 370 of a file with a large header.
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+# This is line 373 of a file with a large header.
+# This is line 374 of a file with a large header.
+# This is line 375 of a file with a large header.
+# This is line 376 of a file with a large header.
+# This is line 377 of a file with a large header.
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+# This is line 387 of a file with a large header.
+# This is line 388 of a file with a large header.
+# This is line 389 of a file with a large header.
+# This is line 390 of a file with a large header.
+# This is line 391 of a file with a large header.
+# This is line 392 of a file with a large header.
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+# This is line 406 of a file with a large header.
+# This is line 407 of a file with a large header.
+# This is line 408 of a file with a large header.
+# This is line 409 of a file with a large header.
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+# This is line 411 of a file with a large header.
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+# This is line 506 of a file with a large header.
+# This is line 507 of a file with a large header.
+# This is line 508 of a file with a large header.
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+# This is line 519 of a file with a large header.
+# This is line 520 of a file with a large header.
+# This is line 521 of a file with a large header.
+# This is line 522 of a file with a large header.
+# This is line 523 of a file with a large header.
+# This is line 524 of a file with a large header.
+# This is line 525 of a file with a large header.
+# This is line 526 of a file with a large header.
+# This is line 527 of a file with a large header.
+# This is line 528 of a file with a large header.
+# This is line 529 of a file with a large header.
+# This is line 530 of a file with a large header.
+# This is line 531 of a file with a large header.
+# This is line 532 of a file with a large header.
+# This is line 533 of a file with a large header.
+# This is line 534 of a file with a large header.
+# This is line 535 of a file with a large header.
+# This is line 536 of a file with a large header.
+# This is line 537 of a file with a large header.
+# This is line 538 of a file with a large header.
+# This is line 539 of a file with a large header.
+# This is line 540 of a file with a large header.
+# This is line 541 of a file with a large header.
+# This is line 542 of a file with a large header.
+# This is line 543 of a file with a large header.
+# This is line 544 of a file with a large header.
+# This is line 545 of a file with a large header.
+# This is line 546 of a file with a large header.
+# This is line 547 of a file with a large header.
+# This is line 548 of a file with a large header.
+# This is line 549 of a file with a large header.
+# This is line 550 of a file with a large header.
+# This is line 551 of a file with a large header.
+# This is line 552 of a file with a large header.
+# This is line 553 of a file with a large header.
+# This is line 554 of a file with a large header.
+# This is line 555 of a file with a large header.
+# This is line 556 of a file with a large header.
+# This is line 557 of a file with a large header.
+# This is line 558 of a file with a large header.
+# This is line 559 of a file with a large header.
+# This is line 560 of a file with a large header.
+# This is line 561 of a file with a large header.
+# This is line 562 of a file with a large header.
+# This is line 563 of a file with a large header.
+# This is line 564 of a file with a large header.
+# This is line 565 of a file with a large header.
+# This is line 566 of a file with a large header.
+# This is line 567 of a file with a large header.
+# This is line 568 of a file with a large header.
+# This is line 569 of a file with a large header.
+# This is line 570 of a file with a large header.
+# This is line 571 of a file with a large header.
+# This is line 572 of a file with a large header.
+# This is line 573 of a file with a large header.
+# This is line 574 of a file with a large header.
+# This is line 575 of a file with a large header.
+# This is line 576 of a file with a large header.
+# This is line 577 of a file with a large header.
+# This is line 578 of a file with a large header.
+# This is line 579 of a file with a large header.
+# This is line 580 of a file with a large header.
+# This is line 581 of a file with a large header.
+# This is line 582 of a file with a large header.
+# This is line 583 of a file with a large header.
+# This is line 584 of a file with a large header.
+# This is line 585 of a file with a large header.
+# This is line 586 of a file with a large header.
+# This is line 587 of a file with a large header.
+# This is line 588 of a file with a large header.
+# This is line 589 of a file with a large header.
+# This is line 590 of a file with a large header.
+# This is line 591 of a file with a large header.
+# This is line 592 of a file with a large header.
+# This is line 593 of a file with a large header.
+# This is line 594 of a file with a large header.
+# This is line 595 of a file with a large header.
+# This is line 596 of a file with a large header.
+# This is line 597 of a file with a large header.
+# This is line 598 of a file with a large header.
+# This is line 599 of a file with a large header.
+# This is line 600 of a file with a large header.
+# This is line 601 of a file with a large header.
+# This is line 602 of a file with a large header.
+# This is line 603 of a file with a large header.
+# This is line 604 of a file with a large header.
+# This is line 605 of a file with a large header.
+# This is line 606 of a file with a large header.
+# This is line 607 of a file with a large header.
+# This is line 608 of a file with a large header.
+# This is line 609 of a file with a large header.
+# This is line 610 of a file with a large header.
+# This is line 611 of a file with a large header.
+# This is line 612 of a file with a large header.
+# This is line 613 of a file with a large header.
+# This is line 614 of a file with a large header.
+# This is line 615 of a file with a large header.
+# This is line 616 of a file with a large header.
+# This is line 617 of a file with a large header.
+# This is line 618 of a file with a large header.
+# This is line 619 of a file with a large header.
+# This is line 620 of a file with a large header.
+# This is line 621 of a file with a large header.
+# This is line 622 of a file with a large header.
+# This is line 623 of a file with a large header.
+# This is line 624 of a file with a large header.
+# This is line 625 of a file with a large header.
+# This is line 626 of a file with a large header.
+# This is line 627 of a file with a large header.
+# This is line 628 of a file with a large header.
+# This is line 629 of a file with a large header.
+# This is line 630 of a file with a large header.
+# This is line 631 of a file with a large header.
+# This is line 632 of a file with a large header.
+# This is line 633 of a file with a large header.
+# This is line 634 of a file with a large header.
+# This is line 635 of a file with a large header.
+# This is line 636 of a file with a large header.
+# This is line 637 of a file with a large header.
+# This is line 638 of a file with a large header.
+# This is line 639 of a file with a large header.
+# This is line 640 of a file with a large header.
+# This is line 641 of a file with a large header.
+# This is line 642 of a file with a large header.
+# This is line 643 of a file with a large header.
+# This is line 644 of a file with a large header.
+# This is line 645 of a file with a large header.
+# This is line 646 of a file with a large header.
+# This is line 647 of a file with a large header.
+# This is line 648 of a file with a large header.
+# This is line 649 of a file with a large header.
+# This is line 650 of a file with a large header.
+# This is line 651 of a file with a large header.
+# This is line 652 of a file with a large header.
+# This is line 653 of a file with a large header.
+# This is line 654 of a file with a large header.
+# This is line 655 of a file with a large header.
+# This is line 656 of a file with a large header.
+# This is line 657 of a file with a large header.
+# This is line 658 of a file with a large header.
+# This is line 659 of a file with a large header.
+# This is line 660 of a file with a large header.
+# This is line 661 of a file with a large header.
+# This is line 662 of a file with a large header.
+# This is line 663 of a file with a large header.
+# This is line 664 of a file with a large header.
+# This is line 665 of a file with a large header.
+# This is line 666 of a file with a large header.
+# This is line 667 of a file with a large header.
+# This is line 668 of a file with a large header.
+# This is line 669 of a file with a large header.
+# This is line 670 of a file with a large header.
+# This is line 671 of a file with a large header.
+# This is line 672 of a file with a large header.
+# This is line 673 of a file with a large header.
+# This is line 674 of a file with a large header.
+# This is line 675 of a file with a large header.
+# This is line 676 of a file with a large header.
+# This is line 677 of a file with a large header.
+# This is line 678 of a file with a large header.
+# This is line 679 of a file with a large header.
+# This is line 680 of a file with a large header.
+# This is line 681 of a file with a large header.
+# This is line 682 of a file with a large header.
+# This is line 683 of a file with a large header.
+# This is line 684 of a file with a large header.
+# This is line 685 of a file with a large header.
+# This is line 686 of a file with a large header.
+# This is line 687 of a file with a large header.
+# This is line 688 of a file with a large header.
+# This is line 689 of a file with a large header.
+# This is line 690 of a file with a large header.
+# This is line 691 of a file with a large header.
+# This is line 692 of a file with a large header.
+# This is line 693 of a file with a large header.
+# This is line 694 of a file with a large header.
+# This is line 695 of a file with a large header.
+# This is line 696 of a file with a large header.
+# This is line 697 of a file with a large header.
+# This is line 698 of a file with a large header.
+# This is line 699 of a file with a large header.
+# This is line 700 of a file with a large header.
+# This is line 701 of a file with a large header.
+# This is line 702 of a file with a large header.
+# This is line 703 of a file with a large header.
+# This is line 704 of a file with a large header.
+# This is line 705 of a file with a large header.
+# This is line 706 of a file with a large header.
+# This is line 707 of a file with a large header.
+# This is line 708 of a file with a large header.
+# This is line 709 of a file with a large header.
+# This is line 710 of a file with a large header.
+# This is line 711 of a file with a large header.
+# This is line 712 of a file with a large header.
+# This is line 713 of a file with a large header.
+# This is line 714 of a file with a large header.
+# This is line 715 of a file with a large header.
+# This is line 716 of a file with a large header.
+# This is line 717 of a file with a large header.
+# This is line 718 of a file with a large header.
+# This is line 719 of a file with a large header.
+# This is line 720 of a file with a large header.
+# This is line 721 of a file with a large header.
+# This is line 722 of a file with a large header.
+# This is line 723 of a file with a large header.
+# This is line 724 of a file with a large header.
+# This is line 725 of a file with a large header.
+# This is line 726 of a file with a large header.
+# This is line 727 of a file with a large header.
+# This is line 728 of a file with a large header.
+# This is line 729 of a file with a large header.
+# This is line 730 of a file with a large header.
+# This is line 731 of a file with a large header.
+# This is line 732 of a file with a large header.
+# This is line 733 of a file with a large header.
+# This is line 734 of a file with a large header.
+# This is line 735 of a file with a large header.
+# This is line 736 of a file with a large header.
+# This is line 737 of a file with a large header.
+# This is line 738 of a file with a large header.
+# This is line 739 of a file with a large header.
+# This is line 740 of a file with a large header.
+# This is line 741 of a file with a large header.
+# This is line 742 of a file with a large header.
+# This is line 743 of a file with a large header.
+# This is line 744 of a file with a large header.
+# This is line 745 of a file with a large header.
+# This is line 746 of a file with a large header.
+# This is line 747 of a file with a large header.
+# This is line 748 of a file with a large header.
+# This is line 749 of a file with a large header.
+# This is line 750 of a file with a large header.
+# This is line 751 of a file with a large header.
+# This is line 752 of a file with a large header.
+# This is line 753 of a file with a large header.
+# This is line 754 of a file with a large header.
+# This is line 755 of a file with a large header.
+# This is line 756 of a file with a large header.
+# This is line 757 of a file with a large header.
+# This is line 758 of a file with a large header.
+# This is line 759 of a file with a large header.
+# This is line 760 of a file with a large header.
+# This is line 761 of a file with a large header.
+# This is line 762 of a file with a large header.
+# This is line 763 of a file with a large header.
+# This is line 764 of a file with a large header.
+# This is line 765 of a file with a large header.
+# This is line 766 of a file with a large header.
+# This is line 767 of a file with a large header.
+# This is line 768 of a file with a large header.
+# This is line 769 of a file with a large header.
+# This is line 770 of a file with a large header.
+# This is line 771 of a file with a large header.
+# This is line 772 of a file with a large header.
+# This is line 773 of a file with a large header.
+# This is line 774 of a file with a large header.
+# This is line 775 of a file with a large header.
+# This is line 776 of a file with a large header.
+# This is line 777 of a file with a large header.
+# This is line 778 of a file with a large header.
+# This is line 779 of a file with a large header.
+# This is line 780 of a file with a large header.
+# This is line 781 of a file with a large header.
+# This is line 782 of a file with a large header.
+# This is line 783 of a file with a large header.
+# This is line 784 of a file with a large header.
+# This is line 785 of a file with a large header.
+# This is line 786 of a file with a large header.
+# This is line 787 of a file with a large header.
+# This is line 788 of a file with a large header.
+# This is line 789 of a file with a large header.
+# This is line 790 of a file with a large header.
+# This is line 791 of a file with a large header.
+# This is line 792 of a file with a large header.
+# This is line 793 of a file with a large header.
+# This is line 794 of a file with a large header.
+# This is line 795 of a file with a large header.
+# This is line 796 of a file with a large header.
+# This is line 797 of a file with a large header.
+# This is line 798 of a file with a large header.
+# This is line 799 of a file with a large header.
+# This is line 800 of a file with a large header.
+# This is line 801 of a file with a large header.
+# This is line 802 of a file with a large header.
+# This is line 803 of a file with a large header.
+# This is line 804 of a file with a large header.
+# This is line 805 of a file with a large header.
+# This is line 806 of a file with a large header.
+# This is line 807 of a file with a large header.
+# This is line 808 of a file with a large header.
+# This is line 809 of a file with a large header.
+# This is line 810 of a file with a large header.
+# This is line 811 of a file with a large header.
+# This is line 812 of a file with a large header.
+# This is line 813 of a file with a large header.
+# This is line 814 of a file with a large header.
+# This is line 815 of a file with a large header.
+# This is line 816 of a file with a large header.
+# This is line 817 of a file with a large header.
+# This is line 818 of a file with a large header.
+# This is line 819 of a file with a large header.
+# This is line 820 of a file with a large header.
+# This is line 821 of a file with a large header.
+# This is line 822 of a file with a large header.
+# This is line 823 of a file with a large header.
+# This is line 824 of a file with a large header.
+# This is line 825 of a file with a large header.
+# This is line 826 of a file with a large header.
+# This is line 827 of a file with a large header.
+# This is line 828 of a file with a large header.
+# This is line 829 of a file with a large header.
+# This is line 830 of a file with a large header.
+# This is line 831 of a file with a large header.
+# This is line 832 of a file with a large header.
+# This is line 833 of a file with a large header.
+# This is line 834 of a file with a large header.
+# This is line 835 of a file with a large header.
+# This is line 836 of a file with a large header.
+# This is line 837 of a file with a large header.
+# This is line 838 of a file with a large header.
+# This is line 839 of a file with a large header.
+# This is line 840 of a file with a large header.
+# This is line 841 of a file with a large header.
+# This is line 842 of a file with a large header.
+# This is line 843 of a file with a large header.
+# This is line 844 of a file with a large header.
+# This is line 845 of a file with a large header.
+# This is line 846 of a file with a large header.
+# This is line 847 of a file with a large header.
+# This is line 848 of a file with a large header.
+# This is line 849 of a file with a large header.
+# This is line 850 of a file with a large header.
+# This is line 851 of a file with a large header.
+# This is line 852 of a file with a large header.
+# This is line 853 of a file with a large header.
+# This is line 854 of a file with a large header.
+# This is line 855 of a file with a large header.
+# This is line 856 of a file with a large header.
+# This is line 857 of a file with a large header.
+# This is line 858 of a file with a large header.
+# This is line 859 of a file with a large header.
+# This is line 860 of a file with a large header.
+# This is line 861 of a file with a large header.
+# This is line 862 of a file with a large header.
+# This is line 863 of a file with a large header.
+# This is line 864 of a file with a large header.
+# This is line 865 of a file with a large header.
+# This is line 866 of a file with a large header.
+# This is line 867 of a file with a large header.
+# This is line 868 of a file with a large header.
+# This is line 869 of a file with a large header.
+# This is line 870 of a file with a large header.
+# This is line 871 of a file with a large header.
+# This is line 872 of a file with a large header.
+# This is line 873 of a file with a large header.
+# This is line 874 of a file with a large header.
+# This is line 875 of a file with a large header.
+# This is line 876 of a file with a large header.
+# This is line 877 of a file with a large header.
+# This is line 878 of a file with a large header.
+# This is line 879 of a file with a large header.
+# This is line 880 of a file with a large header.
+# This is line 881 of a file with a large header.
+# This is line 882 of a file with a large header.
+# This is line 883 of a file with a large header.
+# This is line 884 of a file with a large header.
+# This is line 885 of a file with a large header.
+# This is line 886 of a file with a large header.
+# This is line 887 of a file with a large header.
+# This is line 888 of a file with a large header.
+# This is line 889 of a file with a large header.
+# This is line 890 of a file with a large header.
+# This is line 891 of a file with a large header.
+# This is line 892 of a file with a large header.
+# This is line 893 of a file with a large header.
+# This is line 894 of a file with a large header.
+# This is line 895 of a file with a large header.
+# This is line 896 of a file with a large header.
+# This is line 897 of a file with a large header.
+# This is line 898 of a file with a large header.
+# This is line 899 of a file with a large header.
+# This is line 900 of a file with a large header.
+# This is line 901 of a file with a large header.
+# This is line 902 of a file with a large header.
+# This is line 903 of a file with a large header.
+# This is line 904 of a file with a large header.
+# This is line 905 of a file with a large header.
+# This is line 906 of a file with a large header.
+# This is line 907 of a file with a large header.
+# This is line 908 of a file with a large header.
+# This is line 909 of a file with a large header.
+# This is line 910 of a file with a large header.
+# This is line 911 of a file with a large header.
+# This is line 912 of a file with a large header.
+# This is line 913 of a file with a large header.
+# This is line 914 of a file with a large header.
+# This is line 915 of a file with a large header.
+# This is line 916 of a file with a large header.
+# This is line 917 of a file with a large header.
+# This is line 918 of a file with a large header.
+# This is line 919 of a file with a large header.
+# This is line 920 of a file with a large header.
+# This is line 921 of a file with a large header.
+# This is line 922 of a file with a large header.
+# This is line 923 of a file with a large header.
+# This is line 924 of a file with a large header.
+# This is line 925 of a file with a large header.
+# This is line 926 of a file with a large header.
+# This is line 927 of a file with a large header.
+# This is line 928 of a file with a large header.
+# This is line 929 of a file with a large header.
+# This is line 930 of a file with a large header.
+# This is line 931 of a file with a large header.
+# This is line 932 of a file with a large header.
+# This is line 933 of a file with a large header.
+# This is line 934 of a file with a large header.
+# This is line 935 of a file with a large header.
+# This is line 936 of a file with a large header.
+# This is line 937 of a file with a large header.
+# This is line 938 of a file with a large header.
+# This is line 939 of a file with a large header.
+# This is line 940 of a file with a large header.
+# This is line 941 of a file with a large header.
+# This is line 942 of a file with a large header.
+# This is line 943 of a file with a large header.
+# This is line 944 of a file with a large header.
+# This is line 945 of a file with a large header.
+# This is line 946 of a file with a large header.
+# This is line 947 of a file with a large header.
+# This is line 948 of a file with a large header.
+# This is line 949 of a file with a large header.
+# This is line 950 of a file with a large header.
+# This is line 951 of a file with a large header.
+# This is line 952 of a file with a large header.
+# This is line 953 of a file with a large header.
+# This is line 954 of a file with a large header.
+# This is line 955 of a file with a large header.
+# This is line 956 of a file with a large header.
+# This is line 957 of a file with a large header.
+# This is line 958 of a file with a large header.
+# This is line 959 of a file with a large header.
+# This is line 960 of a file with a large header.
+# This is line 961 of a file with a large header.
+# This is line 962 of a file with a large header.
+# This is line 963 of a file with a large header.
+# This is line 964 of a file with a large header.
+# This is line 965 of a file with a large header.
+# This is line 966 of a file with a large header.
+# This is line 967 of a file with a large header.
+# This is line 968 of a file with a large header.
+# This is line 969 of a file with a large header.
+# This is line 970 of a file with a large header.
+# This is line 971 of a file with a large header.
+# This is line 972 of a file with a large header.
+# This is line 973 of a file with a large header.
+# This is line 974 of a file with a large header.
+# This is line 975 of a file with a large header.
+# This is line 976 of a file with a large header.
+# This is line 977 of a file with a large header.
+# This is line 978 of a file with a large header.
+# This is line 979 of a file with a large header.
+# This is line 980 of a file with a large header.
+# This is line 981 of a file with a large header.
+# This is line 982 of a file with a large header.
+# This is line 983 of a file with a large header.
+# This is line 984 of a file with a large header.
+# This is line 985 of a file with a large header.
+# This is line 986 of a file with a large header.
+# This is line 987 of a file with a large header.
+# This is line 988 of a file with a large header.
+# This is line 989 of a file with a large header.
+# This is line 990 of a file with a large header.
+# This is line 991 of a file with a large header.
+# This is line 992 of a file with a large header.
+# This is line 993 of a file with a large header.
+# This is line 994 of a file with a large header.
+# This is line 995 of a file with a large header.
+# This is line 996 of a file with a large header.
+# This is line 997 of a file with a large header.
+# This is line 998 of a file with a large header.
+# This is line 999 of a file with a large header.
+# This is line 1000 of a file with a large header.
+# This is line 1001 of a file with a large header.
+# This is line 1002 of a file with a large header.
+# This is line 1003 of a file with a large header.
+# This is line 1004 of a file with a large header.
+# This is line 1005 of a file with a large header.
+# This is line 1006 of a file with a large header.
+# This is line 1007 of a file with a large header.
+# This is line 1008 of a file with a large header.
+# This is line 1009 of a file with a large header.
+# This is line 1010 of a file with a large header.
+# This is line 1011 of a file with a large header.
+# This is line 1012 of a file with a large header.
+# This is line 1013 of a file with a large header.
+# This is line 1014 of a file with a large header.
+# This is line 1015 of a file with a large header.
+# This is line 1016 of a file with a large header.
+# This is line 1017 of a file with a large header.
+# This is line 1018 of a file with a large header.
+# This is line 1019 of a file with a large header.
+# This is line 1020 of a file with a large header.
+# This is line 1021 of a file with a large header.
+# This is line 1022 of a file with a large header.
+# This is line 1023 of a file with a large header.
+# This is line 1024 of a file with a large header.
+# This is line 1025 of a file with a large header.
+# This is line 1026 of a file with a large header.
+# This is line 1027 of a file with a large header.
+# This is line 1028 of a file with a large header.
+# This is line 1029 of a file with a large header.
+# This is line 1030 of a file with a large header.
+# This is line 1031 of a file with a large header.
+# This is line 1032 of a file with a large header.
+# This is line 1033 of a file with a large header.
+# This is line 1034 of a file with a large header.
+# This is line 1035 of a file with a large header.
+# This is line 1036 of a file with a large header.
+# This is line 1037 of a file with a large header.
+# This is line 1038 of a file with a large header.
+# This is line 1039 of a file with a large header.
+# This is line 1040 of a file with a large header.
+# This is line 1041 of a file with a large header.
+# This is line 1042 of a file with a large header.
+# This is line 1043 of a file with a large header.
+# This is line 1044 of a file with a large header.
+# This is line 1045 of a file with a large header.
+# This is line 1046 of a file with a large header.
+# This is line 1047 of a file with a large header.
+# This is line 1048 of a file with a large header.
+# This is line 1049 of a file with a large header.
+# This is line 1050 of a file with a large header.
+# This is line 1051 of a file with a large header.
+# This is line 1052 of a file with a large header.
+# This is line 1053 of a file with a large header.
+# This is line 1054 of a file with a large header.
+# This is line 1055 of a file with a large header.
+# This is line 1056 of a file with a large header.
+# This is line 1057 of a file with a large header.
+# This is line 1058 of a file with a large header.
+# This is line 1059 of a file with a large header.
+# This is line 1060 of a file with a large header.
+# This is line 1061 of a file with a large header.
+# This is line 1062 of a file with a large header.
+# This is line 1063 of a file with a large header.
+# This is line 1064 of a file with a large header.
+# This is line 1065 of a file with a large header.
+# This is line 1066 of a file with a large header.
+# This is line 1067 of a file with a large header.
+# This is line 1068 of a file with a large header.
+# This is line 1069 of a file with a large header.
+# This is line 1070 of a file with a large header.
+# This is line 1071 of a file with a large header.
+# This is line 1072 of a file with a large header.
+# This is line 1073 of a file with a large header.
+# This is line 1074 of a file with a large header.
+# This is line 1075 of a file with a large header.
+# This is line 1076 of a file with a large header.
+# This is line 1077 of a file with a large header.
+# This is line 1078 of a file with a large header.
+# This is line 1079 of a file with a large header.
+# This is line 1080 of a file with a large header.
+# This is line 1081 of a file with a large header.
+# This is line 1082 of a file with a large header.
+# This is line 1083 of a file with a large header.
+# This is line 1084 of a file with a large header.
+# This is line 1085 of a file with a large header.
+# This is line 1086 of a file with a large header.
+# This is line 1087 of a file with a large header.
+# This is line 1088 of a file with a large header.
+# This is line 1089 of a file with a large header.
+# This is line 1090 of a file with a large header.
+# This is line 1091 of a file with a large header.
+# This is line 1092 of a file with a large header.
+# This is line 1093 of a file with a large header.
+# This is line 1094 of a file with a large header.
+# This is line 1095 of a file with a large header.
+# This is line 1096 of a file with a large header.
+# This is line 1097 of a file with a large header.
+# This is line 1098 of a file with a large header.
+# This is line 1099 of a file with a large header.
+# This is line 1100 of a file with a large header.
+# This is line 1101 of a file with a large header.
+# This is line 1102 of a file with a large header.
+# This is line 1103 of a file with a large header.
+# This is line 1104 of a file with a large header.
+# This is line 1105 of a file with a large header.
+# This is line 1106 of a file with a large header.
+# This is line 1107 of a file with a large header.
+# This is line 1108 of a file with a large header.
+# This is line 1109 of a file with a large header.
+# This is line 1110 of a file with a large header.
+# This is line 1111 of a file with a large header.
+# This is line 1112 of a file with a large header.
+# This is line 1113 of a file with a large header.
+# This is line 1114 of a file with a large header.
+# This is line 1115 of a file with a large header.
+# This is line 1116 of a file with a large header.
+# This is line 1117 of a file with a large header.
+# This is line 1118 of a file with a large header.
+# This is line 1119 of a file with a large header.
+# This is line 1120 of a file with a large header.
+# This is line 1121 of a file with a large header.
+# This is line 1122 of a file with a large header.
+# This is line 1123 of a file with a large header.
+# This is line 1124 of a file with a large header.
+# This is line 1125 of a file with a large header.
+# This is line 1126 of a file with a large header.
+# This is line 1127 of a file with a large header.
+# This is line 1128 of a file with a large header.
+# This is line 1129 of a file with a large header.
+# This is line 1130 of a file with a large header.
+# This is line 1131 of a file with a large header.
+# This is line 1132 of a file with a large header.
+# This is line 1133 of a file with a large header.
+# This is line 1134 of a file with a large header.
+# This is line 1135 of a file with a large header.
+# This is line 1136 of a file with a large header.
+# This is line 1137 of a file with a large header.
+# This is line 1138 of a file with a large header.
+# This is line 1139 of a file with a large header.
+# This is line 1140 of a file with a large header.
+# This is line 1141 of a file with a large header.
+# This is line 1142 of a file with a large header.
+# This is line 1143 of a file with a large header.
+# This is line 1144 of a file with a large header.
+# This is line 1145 of a file with a large header.
+# This is line 1146 of a file with a large header.
+# This is line 1147 of a file with a large header.
+# This is line 1148 of a file with a large header.
+# This is line 1149 of a file with a large header.
+# This is line 1150 of a file with a large header.
+# This is line 1151 of a file with a large header.
+# This is line 1152 of a file with a large header.
+# This is line 1153 of a file with a large header.
+# This is line 1154 of a file with a large header.
+# This is line 1155 of a file with a large header.
+# This is line 1156 of a file with a large header.
+# This is line 1157 of a file with a large header.
+# This is line 1158 of a file with a large header.
+# This is line 1159 of a file with a large header.
+# This is line 1160 of a file with a large header.
+# This is line 1161 of a file with a large header.
+# This is line 1162 of a file with a large header.
+# This is line 1163 of a file with a large header.
+# This is line 1164 of a file with a large header.
+# This is line 1165 of a file with a large header.
+# This is line 1166 of a file with a large header.
+# This is line 1167 of a file with a large header.
+# This is line 1168 of a file with a large header.
+# This is line 1169 of a file with a large header.
+# This is line 1170 of a file with a large header.
+# This is line 1171 of a file with a large header.
+# This is line 1172 of a file with a large header.
+# This is line 1173 of a file with a large header.
+# This is line 1174 of a file with a large header.
+# This is line 1175 of a file with a large header.
+# This is line 1176 of a file with a large header.
+# This is line 1177 of a file with a large header.
+# This is line 1178 of a file with a large header.
+# This is line 1179 of a file with a large header.
+# This is line 1180 of a file with a large header.
+# This is line 1181 of a file with a large header.
+# This is line 1182 of a file with a large header.
+# This is line 1183 of a file with a large header.
+# This is line 1184 of a file with a large header.
+# This is line 1185 of a file with a large header.
+# This is line 1186 of a file with a large header.
+# This is line 1187 of a file with a large header.
+# This is line 1188 of a file with a large header.
+# This is line 1189 of a file with a large header.
+# This is line 1190 of a file with a large header.
+# This is line 1191 of a file with a large header.
+# This is line 1192 of a file with a large header.
+# This is line 1193 of a file with a large header.
+# This is line 1194 of a file with a large header.
+# This is line 1195 of a file with a large header.
+# This is line 1196 of a file with a large header.
+# This is line 1197 of a file with a large header.
+# This is line 1198 of a file with a large header.
+# This is line 1199 of a file with a large header.
+# This is line 1200 of a file with a large header.
+# This is line 1201 of a file with a large header.
+# This is line 1202 of a file with a large header.
+# This is line 1203 of a file with a large header.
+# This is line 1204 of a file with a large header.
+# This is line 1205 of a file with a large header.
+# This is line 1206 of a file with a large header.
+# This is line 1207 of a file with a large header.
+# This is line 1208 of a file with a large header.
+# This is line 1209 of a file with a large header.
+# This is line 1210 of a file with a large header.
+# This is line 1211 of a file with a large header.
+# This is line 1212 of a file with a large header.
+# This is line 1213 of a file with a large header.
+# This is line 1214 of a file with a large header.
+# This is line 1215 of a file with a large header.
+# This is line 1216 of a file with a large header.
+# This is line 1217 of a file with a large header.
+# This is line 1218 of a file with a large header.
+# This is line 1219 of a file with a large header.
+# This is line 1220 of a file with a large header.
+# This is line 1221 of a file with a large header.
+# This is line 1222 of a file with a large header.
+# This is line 1223 of a file with a large header.
+# This is line 1224 of a file with a large header.
+# This is line 1225 of a file with a large header.
+# This is line 1226 of a file with a large header.
+# This is line 1227 of a file with a large header.
+# This is line 1228 of a file with a large header.
+# This is line 1229 of a file with a large header.
+# This is line 1230 of a file with a large header.
+# This is line 1231 of a file with a large header.
+# This is line 1232 of a file with a large header.
+# This is line 1233 of a file with a large header.
+# This is line 1234 of a file with a large header.
+# This is line 1235 of a file with a large header.
+# This is line 1236 of a file with a large header.
+# This is line 1237 of a file with a large header.
+# This is line 1238 of a file with a large header.
+# This is line 1239 of a file with a large header.
+# This is line 1240 of a file with a large header.
+# This is line 1241 of a file with a large header.
+# This is line 1242 of a file with a large header.
+# This is line 1243 of a file with a large header.
+# This is line 1244 of a file with a large header.
+# This is line 1245 of a file with a large header.
+# This is line 1246 of a file with a large header.
+# This is line 1247 of a file with a large header.
+# This is line 1248 of a file with a large header.
+# This is line 1249 of a file with a large header.
+# This is line 1250 of a file with a large header.
+# This is line 1251 of a file with a large header.
+# This is line 1252 of a file with a large header.
+# This is line 1253 of a file with a large header.
+# This is line 1254 of a file with a large header.
+# This is line 1255 of a file with a large header.
+# This is line 1256 of a file with a large header.
+# This is line 1257 of a file with a large header.
+# This is line 1258 of a file with a large header.
+# This is line 1259 of a file with a large header.
+# This is line 1260 of a file with a large header.
+# This is line 1261 of a file with a large header.
+# This is line 1262 of a file with a large header.
+# This is line 1263 of a file with a large header.
+# This is line 1264 of a file with a large header.
+# This is line 1265 of a file with a large header.
+# This is line 1266 of a file with a large header.
+# This is line 1267 of a file with a large header.
+# This is line 1268 of a file with a large header.
+# This is line 1269 of a file with a large header.
+# This is line 1270 of a file with a large header.
+# This is line 1271 of a file with a large header.
+# This is line 1272 of a file with a large header.
+# This is line 1273 of a file with a large header.
+# This is line 1274 of a file with a large header.
+# This is line 1275 of a file with a large header.
+# This is line 1276 of a file with a large header.
+# This is line 1277 of a file with a large header.
+# This is line 1278 of a file with a large header.
+# This is line 1279 of a file with a large header.
+# This is line 1280 of a file with a large header.
+# This is line 1281 of a file with a large header.
+# This is line 1282 of a file with a large header.
+# This is line 1283 of a file with a large header.
+# This is line 1284 of a file with a large header.
+# This is line 1285 of a file with a large header.
+# This is line 1286 of a file with a large header.
+# This is line 1287 of a file with a large header.
+# This is line 1288 of a file with a large header.
+# This is line 1289 of a file with a large header.
+# This is line 1290 of a file with a large header.
+# This is line 1291 of a file with a large header.
+# This is line 1292 of a file with a large header.
+# This is line 1293 of a file with a large header.
+# This is line 1294 of a file with a large header.
+# This is line 1295 of a file with a large header.
+# This is line 1296 of a file with a large header.
+# This is line 1297 of a file with a large header.
+# This is line 1298 of a file with a large header.
+# This is line 1299 of a file with a large header.
+# This is line 1300 of a file with a large header.
+# This is line 1301 of a file with a large header.
+# This is line 1302 of a file with a large header.
+# This is line 1303 of a file with a large header.
+# This is line 1304 of a file with a large header.
+# This is line 1305 of a file with a large header.
+# This is line 1306 of a file with a large header.
+# This is line 1307 of a file with a large header.
+# This is line 1308 of a file with a large header.
+# This is line 1309 of a file with a large header.
+# This is line 1310 of a file with a large header.
+# This is line 1311 of a file with a large header.
+# This is line 1312 of a file with a large header.
+# This is line 1313 of a file with a large header.
+# This is line 1314 of a file with a large header.
+# This is line 1315 of a file with a large header.
+# This is line 1316 of a file with a large header.
+# This is line 1317 of a file with a large header.
+# This is line 1318 of a file with a large header.
+# This is line 1319 of a file with a large header.
+# This is line 1320 of a file with a large header.
+# This is line 1321 of a file with a large header.
+# This is line 1322 of a file with a large header.
+# This is line 1323 of a file with a large header.
+# This is line 1324 of a file with a large header.
+# This is line 1325 of a file with a large header.
+# This is line 1326 of a file with a large header.
+# This is line 1327 of a file with a large header.
+# This is line 1328 of a file with a large header.
+# This is line 1329 of a file with a large header.
+# This is line 1330 of a file with a large header.
+# This is line 1331 of a file with a large header.
+# This is line 1332 of a file with a large header.
+# This is line 1333 of a file with a large header.
+# This is line 1334 of a file with a large header.
+# This is line 1335 of a file with a large header.
+# This is line 1336 of a file with a large header.
+# This is line 1337 of a file with a large header.
+# This is line 1338 of a file with a large header.
+# This is line 1339 of a file with a large header.
+# This is line 1340 of a file with a large header.
+# This is line 1341 of a file with a large header.
+# This is line 1342 of a file with a large header.
+# This is line 1343 of a file with a large header.
+# This is line 1344 of a file with a large header.
+# This is line 1345 of a file with a large header.
+# This is line 1346 of a file with a large header.
+# This is line 1347 of a file with a large header.
+# This is line 1348 of a file with a large header.
+# This is line 1349 of a file with a large header.
+# This is line 1350 of a file with a large header.
+# This is line 1351 of a file with a large header.
+# This is line 1352 of a file with a large header.
+# This is line 1353 of a file with a large header.
+# This is line 1354 of a file with a large header.
+# This is line 1355 of a file with a large header.
+# This is line 1356 of a file with a large header.
+# This is line 1357 of a file with a large header.
+# This is line 1358 of a file with a large header.
+# This is line 1359 of a file with a large header.
+# This is line 1360 of a file with a large header.
+# This is line 1361 of a file with a large header.
+# This is line 1362 of a file with a large header.
+# This is line 1363 of a file with a large header.
+# This is line 1364 of a file with a large header.
+# This is line 1365 of a file with a large header.
+# This is line 1366 of a file with a large header.
+# This is line 1367 of a file with a large header.
+# This is line 1368 of a file with a large header.
+# This is line 1369 of a file with a large header.
+# This is line 1370 of a file with a large header.
+# This is line 1371 of a file with a large header.
+# This is line 1372 of a file with a large header.
+# This is line 1373 of a file with a large header.
+# This is line 1374 of a file with a large header.
+# This is line 1375 of a file with a large header.
+# This is line 1376 of a file with a large header.
+# This is line 1377 of a file with a large header.
+# This is line 1378 of a file with a large header.
+# This is line 1379 of a file with a large header.
+# This is line 1380 of a file with a large header.
+# This is line 1381 of a file with a large header.
+# This is line 1382 of a file with a large header.
+# This is line 1383 of a file with a large header.
+# This is line 1384 of a file with a large header.
+# This is line 1385 of a file with a large header.
+# This is line 1386 of a file with a large header.
+# This is line 1387 of a file with a large header.
+# This is line 1388 of a file with a large header.
+# This is line 1389 of a file with a large header.
+# This is line 1390 of a file with a large header.
+# This is line 1391 of a file with a large header.
+# This is line 1392 of a file with a large header.
+# This is line 1393 of a file with a large header.
+# This is line 1394 of a file with a large header.
+# This is line 1395 of a file with a large header.
+# This is line 1396 of a file with a large header.
+# This is line 1397 of a file with a large header.
+# This is line 1398 of a file with a large header.
+# This is line 1399 of a file with a large header.
+# This is line 1400 of a file with a large header.
+# This is line 1401 of a file with a large header.
+# This is line 1402 of a file with a large header.
+# This is line 1403 of a file with a large header.
+# This is line 1404 of a file with a large header.
+# This is line 1405 of a file with a large header.
+# This is line 1406 of a file with a large header.
+# This is line 1407 of a file with a large header.
+# This is line 1408 of a file with a large header.
+# This is line 1409 of a file with a large header.
+# This is line 1410 of a file with a large header.
+# This is line 1411 of a file with a large header.
+# This is line 1412 of a file with a large header.
+# This is line 1413 of a file with a large header.
+# This is line 1414 of a file with a large header.
+# This is line 1415 of a file with a large header.
+# This is line 1416 of a file with a large header.
+# This is line 1417 of a file with a large header.
+# This is line 1418 of a file with a large header.
+# This is line 1419 of a file with a large header.
+# This is line 1420 of a file with a large header.
+# This is line 1421 of a file with a large header.
+# This is line 1422 of a file with a large header.
+# This is line 1423 of a file with a large header.
+# This is line 1424 of a file with a large header.
+# This is line 1425 of a file with a large header.
+# This is line 1426 of a file with a large header.
+# This is line 1427 of a file with a large header.
+# This is line 1428 of a file with a large header.
+# This is line 1429 of a file with a large header.
+# This is line 1430 of a file with a large header.
+# This is line 1431 of a file with a large header.
+# This is line 1432 of a file with a large header.
+# This is line 1433 of a file with a large header.
+# This is line 1434 of a file with a large header.
+# This is line 1435 of a file with a large header.
+# This is line 1436 of a file with a large header.
+# This is line 1437 of a file with a large header.
+# This is line 1438 of a file with a large header.
+# This is line 1439 of a file with a large header.
+# This is line 1440 of a file with a large header.
+# This is line 1441 of a file with a large header.
+# This is line 1442 of a file with a large header.
+# This is line 1443 of a file with a large header.
+# This is line 1444 of a file with a large header.
+# This is line 1445 of a file with a large header.
+# This is line 1446 of a file with a large header.
+# This is line 1447 of a file with a large header.
+# This is line 1448 of a file with a large header.
+# This is line 1449 of a file with a large header.
+# This is line 1450 of a file with a large header.
+# This is line 1451 of a file with a large header.
+# This is line 1452 of a file with a large header.
+# This is line 1453 of a file with a large header.
+# This is line 1454 of a file with a large header.
+# This is line 1455 of a file with a large header.
+# This is line 1456 of a file with a large header.
+# This is line 1457 of a file with a large header.
+# This is line 1458 of a file with a large header.
+# This is line 1459 of a file with a large header.
+# This is line 1460 of a file with a large header.
+# This is line 1461 of a file with a large header.
+# This is line 1462 of a file with a large header.
+# This is line 1463 of a file with a large header.
+# This is line 1464 of a file with a large header.
+# This is line 1465 of a file with a large header.
+# This is line 1466 of a file with a large header.
+# This is line 1467 of a file with a large header.
+# This is line 1468 of a file with a large header.
+# This is line 1469 of a file with a large header.
+# This is line 1470 of a file with a large header.
+# This is line 1471 of a file with a large header.
+# This is line 1472 of a file with a large header.
+# This is line 1473 of a file with a large header.
+# This is line 1474 of a file with a large header.
+# This is line 1475 of a file with a large header.
+# This is line 1476 of a file with a large header.
+# This is line 1477 of a file with a large header.
+# This is line 1478 of a file with a large header.
+# This is line 1479 of a file with a large header.
+# This is line 1480 of a file with a large header.
+# This is line 1481 of a file with a large header.
+# This is line 1482 of a file with a large header.
+# This is line 1483 of a file with a large header.
+# This is line 1484 of a file with a large header.
+# This is line 1485 of a file with a large header.
+# This is line 1486 of a file with a large header.
+# This is line 1487 of a file with a large header.
+# This is line 1488 of a file with a large header.
+# This is line 1489 of a file with a large header.
+# This is line 1490 of a file with a large header.
+# This is line 1491 of a file with a large header.
+# This is line 1492 of a file with a large header.
+# This is line 1493 of a file with a large header.
+# This is line 1494 of a file with a large header.
+# This is line 1495 of a file with a large header.
+# This is line 1496 of a file with a large header.
+# This is line 1497 of a file with a large header.
+# This is line 1498 of a file with a large header.
+# This is line 1499 of a file with a large header.
+# This is line 1500 of a file with a large header.
+# This is line 1501 of a file with a large header.
+# This is line 1502 of a file with a large header.
+# This is line 1503 of a file with a large header.
+# This is line 1504 of a file with a large header.
+# This is line 1505 of a file with a large header.
+# This is line 1506 of a file with a large header.
+# This is line 1507 of a file with a large header.
+# This is line 1508 of a file with a large header.
+# This is line 1509 of a file with a large header.
+# This is line 1510 of a file with a large header.
+# This is line 1511 of a file with a large header.
+# This is line 1512 of a file with a large header.
+# This is line 1513 of a file with a large header.
+# This is line 1514 of a file with a large header.
+# This is line 1515 of a file with a large header.
+# This is line 1516 of a file with a large header.
+# This is line 1517 of a file with a large header.
+# This is line 1518 of a file with a large header.
+# This is line 1519 of a file with a large header.
+# This is line 1520 of a file with a large header.
+# This is line 1521 of a file with a large header.
+# This is line 1522 of a file with a large header.
+# This is line 1523 of a file with a large header.
+# This is line 1524 of a file with a large header.
+# This is line 1525 of a file with a large header.
+# This is line 1526 of a file with a large header.
+# This is line 1527 of a file with a large header.
+# This is line 1528 of a file with a large header.
+# This is line 1529 of a file with a large header.
+# This is line 1530 of a file with a large header.
+# This is line 1531 of a file with a large header.
+# This is line 1532 of a file with a large header.
+# This is line 1533 of a file with a large header.
+# This is line 1534 of a file with a large header.
+# This is line 1535 of a file with a large header.
+# This is line 1536 of a file with a large header.
+# This is line 1537 of a file with a large header.
+# This is line 1538 of a file with a large header.
+# This is line 1539 of a file with a large header.
+# This is line 1540 of a file with a large header.
+# This is line 1541 of a file with a large header.
+# This is line 1542 of a file with a large header.
+# This is line 1543 of a file with a large header.
+# This is line 1544 of a file with a large header.
+# This is line 1545 of a file with a large header.
+# This is line 1546 of a file with a large header.
+# This is line 1547 of a file with a large header.
+# This is line 1548 of a file with a large header.
+# This is line 1549 of a file with a large header.
+# This is line 1550 of a file with a large header.
+# This is line 1551 of a file with a large header.
+# This is line 1552 of a file with a large header.
+# This is line 1553 of a file with a large header.
+# This is line 1554 of a file with a large header.
+# This is line 1555 of a file with a large header.
+# This is line 1556 of a file with a large header.
+# This is line 1557 of a file with a large header.
+# This is line 1558 of a file with a large header.
+# This is line 1559 of a file with a large header.
+# This is line 1560 of a file with a large header.
+# This is line 1561 of a file with a large header.
+# This is line 1562 of a file with a large header.
+# This is line 1563 of a file with a large header.
+# This is line 1564 of a file with a large header.
+# This is line 1565 of a file with a large header.
+# This is line 1566 of a file with a large header.
+# This is line 1567 of a file with a large header.
+# This is line 1568 of a file with a large header.
+# This is line 1569 of a file with a large header.
+# This is line 1570 of a file with a large header.
+# This is line 1571 of a file with a large header.
+# This is line 1572 of a file with a large header.
+# This is line 1573 of a file with a large header.
+# This is line 1574 of a file with a large header.
+# This is line 1575 of a file with a large header.
+# This is line 1576 of a file with a large header.
+# This is line 1577 of a file with a large header.
+# This is line 1578 of a file with a large header.
+# This is line 1579 of a file with a large header.
+# This is line 1580 of a file with a large header.
+# This is line 1581 of a file with a large header.
+# This is line 1582 of a file with a large header.
+# This is line 1583 of a file with a large header.
+# This is line 1584 of a file with a large header.
+# This is line 1585 of a file with a large header.
+# This is line 1586 of a file with a large header.
+# This is line 1587 of a file with a large header.
+# This is line 1588 of a file with a large header.
+# This is line 1589 of a file with a large header.
+# This is line 1590 of a file with a large header.
+# This is line 1591 of a file with a large header.
+# This is line 1592 of a file with a large header.
+# This is line 1593 of a file with a large header.
+# This is line 1594 of a file with a large header.
+# This is line 1595 of a file with a large header.
+# This is line 1596 of a file with a large header.
+# This is line 1597 of a file with a large header.
+# This is line 1598 of a file with a large header.
+# This is line 1599 of a file with a large header.
+# This is line 1600 of a file with a large header.
+# This is line 1601 of a file with a large header.
+# This is line 1602 of a file with a large header.
+# This is line 1603 of a file with a large header.
+# This is line 1604 of a file with a large header.
+# This is line 1605 of a file with a large header.
+# This is line 1606 of a file with a large header.
+# This is line 1607 of a file with a large header.
+# This is line 1608 of a file with a large header.
+# This is line 1609 of a file with a large header.
+# This is line 1610 of a file with a large header.
+# This is line 1611 of a file with a large header.
+# This is line 1612 of a file with a large header.
+# This is line 1613 of a file with a large header.
+# This is line 1614 of a file with a large header.
+# This is line 1615 of a file with a large header.
+# This is line 1616 of a file with a large header.
+# This is line 1617 of a file with a large header.
+# This is line 1618 of a file with a large header.
+# This is line 1619 of a file with a large header.
+# This is line 1620 of a file with a large header.
+# This is line 1621 of a file with a large header.
+# This is line 1622 of a file with a large header.
+# This is line 1623 of a file with a large header.
+# This is line 1624 of a file with a large header.
+# This is line 1625 of a file with a large header.
+# This is line 1626 of a file with a large header.
+# This is line 1627 of a file with a large header.
+# This is line 1628 of a file with a large header.
+# This is line 1629 of a file with a large header.
+# This is line 1630 of a file with a large header.
+# This is line 1631 of a file with a large header.
+# This is line 1632 of a file with a large header.
+# This is line 1633 of a file with a large header.
+# This is line 1634 of a file with a large header.
+# This is line 1635 of a file with a large header.
+# This is line 1636 of a file with a large header.
+# This is line 1637 of a file with a large header.
+# This is line 1638 of a file with a large header.
+# This is line 1639 of a file with a large header.
+# This is line 1640 of a file with a large header.
+# This is line 1641 of a file with a large header.
+# This is line 1642 of a file with a large header.
+# This is line 1643 of a file with a large header.
+# This is line 1644 of a file with a large header.
+# This is line 1645 of a file with a large header.
+# This is line 1646 of a file with a large header.
+# This is line 1647 of a file with a large header.
+# This is line 1648 of a file with a large header.
+# This is line 1649 of a file with a large header.
+# This is line 1650 of a file with a large header.
+# This is line 1651 of a file with a large header.
+# This is line 1652 of a file with a large header.
+# This is line 1653 of a file with a large header.
+# This is line 1654 of a file with a large header.
+# This is line 1655 of a file with a large header.
+# This is line 1656 of a file with a large header.
+# This is line 1657 of a file with a large header.
+# This is line 1658 of a file with a large header.
+# This is line 1659 of a file with a large header.
+# This is line 1660 of a file with a large header.
+# This is line 1661 of a file with a large header.
+# This is line 1662 of a file with a large header.
+# This is line 1663 of a file with a large header.
+# This is line 1664 of a file with a large header.
+# This is line 1665 of a file with a large header.
+# This is line 1666 of a file with a large header.
+# This is line 1667 of a file with a large header.
+# This is line 1668 of a file with a large header.
+# This is line 1669 of a file with a large header.
+# This is line 1670 of a file with a large header.
+# This is line 1671 of a file with a large header.
+# This is line 1672 of a file with a large header.
+# This is line 1673 of a file with a large header.
+# This is line 1674 of a file with a large header.
+# This is line 1675 of a file with a large header.
+# This is line 1676 of a file with a large header.
+# This is line 1677 of a file with a large header.
+# This is line 1678 of a file with a large header.
+# This is line 1679 of a file with a large header.
+# This is line 1680 of a file with a large header.
+# This is line 1681 of a file with a large header.
+# This is line 1682 of a file with a large header.
+# This is line 1683 of a file with a large header.
+# This is line 1684 of a file with a large header.
+# This is line 1685 of a file with a large header.
+# This is line 1686 of a file with a large header.
+# This is line 1687 of a file with a large header.
+# This is line 1688 of a file with a large header.
+# This is line 1689 of a file with a large header.
+# This is line 1690 of a file with a large header.
+# This is line 1691 of a file with a large header.
+# This is line 1692 of a file with a large header.
+# This is line 1693 of a file with a large header.
+# This is line 1694 of a file with a large header.
+# This is line 1695 of a file with a large header.
+# This is line 1696 of a file with a large header.
+# This is line 1697 of a file with a large header.
+# This is line 1698 of a file with a large header.
+# This is line 1699 of a file with a large header.
+# This is line 1700 of a file with a large header.
+# This is line 1701 of a file with a large header.
+# This is line 1702 of a file with a large header.
+# This is line 1703 of a file with a large header.
+# This is line 1704 of a file with a large header.
+# This is line 1705 of a file with a large header.
+# This is line 1706 of a file with a large header.
+# This is line 1707 of a file with a large header.
+# This is line 1708 of a file with a large header.
+# This is line 1709 of a file with a large header.
+# This is line 1710 of a file with a large header.
+# This is line 1711 of a file with a large header.
+# This is line 1712 of a file with a large header.
+# This is line 1713 of a file with a large header.
+# This is line 1714 of a file with a large header.
+# This is line 1715 of a file with a large header.
+# This is line 1716 of a file with a large header.
+# This is line 1717 of a file with a large header.
+# This is line 1718 of a file with a large header.
+# This is line 1719 of a file with a large header.
+# This is line 1720 of a file with a large header.
+# This is line 1721 of a file with a large header.
+# This is line 1722 of a file with a large header.
+# This is line 1723 of a file with a large header.
+# This is line 1724 of a file with a large header.
+# This is line 1725 of a file with a large header.
+# This is line 1726 of a file with a large header.
+# This is line 1727 of a file with a large header.
+# This is line 1728 of a file with a large header.
+# This is line 1729 of a file with a large header.
+# This is line 1730 of a file with a large header.
+# This is line 1731 of a file with a large header.
+# This is line 1732 of a file with a large header.
+# This is line 1733 of a file with a large header.
+# This is line 1734 of a file with a large header.
+# This is line 1735 of a file with a large header.
+# This is line 1736 of a file with a large header.
+# This is line 1737 of a file with a large header.
+# This is line 1738 of a file with a large header.
+# This is line 1739 of a file with a large header.
+# This is line 1740 of a file with a large header.
+# This is line 1741 of a file with a large header.
+# This is line 1742 of a file with a large header.
+# This is line 1743 of a file with a large header.
+# This is line 1744 of a file with a large header.
+# This is line 1745 of a file with a large header.
+# This is line 1746 of a file with a large header.
+# This is line 1747 of a file with a large header.
+# This is line 1748 of a file with a large header.
+# This is line 1749 of a file with a large header.
+# This is line 1750 of a file with a large header.
+# This is line 1751 of a file with a large header.
+# This is line 1752 of a file with a large header.
+# This is line 1753 of a file with a large header.
+# This is line 1754 of a file with a large header.
+# This is line 1755 of a file with a large header.
+# This is line 1756 of a file with a large header.
+# This is line 1757 of a file with a large header.
+# This is line 1758 of a file with a large header.
+# This is line 1759 of a file with a large header.
+# This is line 1760 of a file with a large header.
+# This is line 1761 of a file with a large header.
+# This is line 1762 of a file with a large header.
+# This is line 1763 of a file with a large header.
+# This is line 1764 of a file with a large header.
+# This is line 1765 of a file with a large header.
+# This is line 1766 of a file with a large header.
+# This is line 1767 of a file with a large header.
+# This is line 1768 of a file with a large header.
+# This is line 1769 of a file with a large header.
+# This is line 1770 of a file with a large header.
+# This is line 1771 of a file with a large header.
+# This is line 1772 of a file with a large header.
+# This is line 1773 of a file with a large header.
+# This is line 1774 of a file with a large header.
+# This is line 1775 of a file with a large header.
+# This is line 1776 of a file with a large header.
+# This is line 1777 of a file with a large header.
+# This is line 1778 of a file with a large header.
+# This is line 1779 of a file with a large header.
+# This is line 1780 of a file with a large header.
+# This is line 1781 of a file with a large header.
+# This is line 1782 of a file with a large header.
+# This is line 1783 of a file with a large header.
+# This is line 1784 of a file with a large header.
+# This is line 1785 of a file with a large header.
+# This is line 1786 of a file with a large header.
+# This is line 1787 of a file with a large header.
+# This is line 1788 of a file with a large header.
+# This is line 1789 of a file with a large header.
+# This is line 1790 of a file with a large header.
+# This is line 1791 of a file with a large header.
+# This is line 1792 of a file with a large header.
+# This is line 1793 of a file with a large header.
+# This is line 1794 of a file with a large header.
+# This is line 1795 of a file with a large header.
+# This is line 1796 of a file with a large header.
+# This is line 1797 of a file with a large header.
+# This is line 1798 of a file with a large header.
+# This is line 1799 of a file with a large header.
+# This is line 1800 of a file with a large header.
+# This is line 1801 of a file with a large header.
+# This is line 1802 of a file with a large header.
+# This is line 1803 of a file with a large header.
+# This is line 1804 of a file with a large header.
+# This is line 1805 of a file with a large header.
+# This is line 1806 of a file with a large header.
+# This is line 1807 of a file with a large header.
+# This is line 1808 of a file with a large header.
+# This is line 1809 of a file with a large header.
+# This is line 1810 of a file with a large header.
+# This is line 1811 of a file with a large header.
+# This is line 1812 of a file with a large header.
+# This is line 1813 of a file with a large header.
+# This is line 1814 of a file with a large header.
+# This is line 1815 of a file with a large header.
+# This is line 1816 of a file with a large header.
+# This is line 1817 of a file with a large header.
+# This is line 1818 of a file with a large header.
+# This is line 1819 of a file with a large header.
+# This is line 1820 of a file with a large header.
+# This is line 1821 of a file with a large header.
+# This is line 1822 of a file with a large header.
+# This is line 1823 of a file with a large header.
+# This is line 1824 of a file with a large header.
+# This is line 1825 of a file with a large header.
+# This is line 1826 of a file with a large header.
+# This is line 1827 of a file with a large header.
+# This is line 1828 of a file with a large header.
+# This is line 1829 of a file with a large header.
+# This is line 1830 of a file with a large header.
+# This is line 1831 of a file with a large header.
+# This is line 1832 of a file with a large header.
+# This is line 1833 of a file with a large header.
+# This is line 1834 of a file with a large header.
+# This is line 1835 of a file with a large header.
+# This is line 1836 of a file with a large header.
+# This is line 1837 of a file with a large header.
+# This is line 1838 of a file with a large header.
+# This is line 1839 of a file with a large header.
+# This is line 1840 of a file with a large header.
+# This is line 1841 of a file with a large header.
+# This is line 1842 of a file with a large header.
+# This is line 1843 of a file with a large header.
+# This is line 1844 of a file with a large header.
+# This is line 1845 of a file with a large header.
+# This is line 1846 of a file with a large header.
+# This is line 1847 of a file with a large header.
+# This is line 1848 of a file with a large header.
+# This is line 1849 of a file with a large header.
+# This is line 1850 of a file with a large header.
+# This is line 1851 of a file with a large header.
+# This is line 1852 of a file with a large header.
+# This is line 1853 of a file with a large header.
+# This is line 1854 of a file with a large header.
+# This is line 1855 of a file with a large header.
+# This is line 1856 of a file with a large header.
+# This is line 1857 of a file with a large header.
+# This is line 1858 of a file with a large header.
+# This is line 1859 of a file with a large header.
+# This is line 1860 of a file with a large header.
+# This is line 1861 of a file with a large header.
+# This is line 1862 of a file with a large header.
+# This is line 1863 of a file with a large header.
+# This is line 1864 of a file with a large header.
+# This is line 1865 of a file with a large header.
+# This is line 1866 of a file with a large header.
+# This is line 1867 of a file with a large header.
+# This is line 1868 of a file with a large header.
+# This is line 1869 of a file with a large header.
+# This is line 1870 of a file with a large header.
+# This is line 1871 of a file with a large header.
+# This is line 1872 of a file with a large header.
+# This is line 1873 of a file with a large header.
+# This is line 1874 of a file with a large header.
+# This is line 1875 of a file with a large header.
+# This is line 1876 of a file with a large header.
+# This is line 1877 of a file with a large header.
+# This is line 1878 of a file with a large header.
+# This is line 1879 of a file with a large header.
+# This is line 1880 of a file with a large header.
+# This is line 1881 of a file with a large header.
+# This is line 1882 of a file with a large header.
+# This is line 1883 of a file with a large header.
+# This is line 1884 of a file with a large header.
+# This is line 1885 of a file with a large header.
+# This is line 1886 of a file with a large header.
+# This is line 1887 of a file with a large header.
+# This is line 1888 of a file with a large header.
+# This is line 1889 of a file with a large header.
+# This is line 1890 of a file with a large header.
+# This is line 1891 of a file with a large header.
+# This is line 1892 of a file with a large header.
+# This is line 1893 of a file with a large header.
+# This is line 1894 of a file with a large header.
+# This is line 1895 of a file with a large header.
+# This is line 1896 of a file with a large header.
+# This is line 1897 of a file with a large header.
+# This is line 1898 of a file with a large header.
+# This is line 1899 of a file with a large header.
+# This is line 1900 of a file with a large header.
+# This is line 1901 of a file with a large header.
+# This is line 1902 of a file with a large header.
+# This is line 1903 of a file with a large header.
+# This is line 1904 of a file with a large header.
+# This is line 1905 of a file with a large header.
+# This is line 1906 of a file with a large header.
+# This is line 1907 of a file with a large header.
+# This is line 1908 of a file with a large header.
+# This is line 1909 of a file with a large header.
+# This is line 1910 of a file with a large header.
+# This is line 1911 of a file with a large header.
+# This is line 1912 of a file with a large header.
+# This is line 1913 of a file with a large header.
+# This is line 1914 of a file with a large header.
+# This is line 1915 of a file with a large header.
+# This is line 1916 of a file with a large header.
+# This is line 1917 of a file with a large header.
+# This is line 1918 of a file with a large header.
+# This is line 1919 of a file with a large header.
+# This is line 1920 of a file with a large header.
+# This is line 1921 of a file with a large header.
+# This is line 1922 of a file with a large header.
+# This is line 1923 of a file with a large header.
+# This is line 1924 of a file with a large header.
+# This is line 1925 of a file with a large header.
+# This is line 1926 of a file with a large header.
+# This is line 1927 of a file with a large header.
+# This is line 1928 of a file with a large header.
+# This is line 1929 of a file with a large header.
+# This is line 1930 of a file with a large header.
+# This is line 1931 of a file with a large header.
+# This is line 1932 of a file with a large header.
+# This is line 1933 of a file with a large header.
+# This is line 1934 of a file with a large header.
+# This is line 1935 of a file with a large header.
+# This is line 1936 of a file with a large header.
+# This is line 1937 of a file with a large header.
+# This is line 1938 of a file with a large header.
+# This is line 1939 of a file with a large header.
+# This is line 1940 of a file with a large header.
+# This is line 1941 of a file with a large header.
+# This is line 1942 of a file with a large header.
+# This is line 1943 of a file with a large header.
+# This is line 1944 of a file with a large header.
+# This is line 1945 of a file with a large header.
+# This is line 1946 of a file with a large header.
+# This is line 1947 of a file with a large header.
+# This is line 1948 of a file with a large header.
+# This is line 1949 of a file with a large header.
+# This is line 1950 of a file with a large header.
+# This is line 1951 of a file with a large header.
+# This is line 1952 of a file with a large header.
+# This is line 1953 of a file with a large header.
+# This is line 1954 of a file with a large header.
+# This is line 1955 of a file with a large header.
+# This is line 1956 of a file with a large header.
+# This is line 1957 of a file with a large header.
+# This is line 1958 of a file with a large header.
+# This is line 1959 of a file with a large header.
+# This is line 1960 of a file with a large header.
+# This is line 1961 of a file with a large header.
+# This is line 1962 of a file with a large header.
+# This is line 1963 of a file with a large header.
+# This is line 1964 of a file with a large header.
+# This is line 1965 of a file with a large header.
+# This is line 1966 of a file with a large header.
+# This is line 1967 of a file with a large header.
+# This is line 1968 of a file with a large header.
+# This is line 1969 of a file with a large header.
+# This is line 1970 of a file with a large header.
+# This is line 1971 of a file with a large header.
+# This is line 1972 of a file with a large header.
+# This is line 1973 of a file with a large header.
+# This is line 1974 of a file with a large header.
+# This is line 1975 of a file with a large header.
+# This is line 1976 of a file with a large header.
+# This is line 1977 of a file with a large header.
+# This is line 1978 of a file with a large header.
+# This is line 1979 of a file with a large header.
+# This is line 1980 of a file with a large header.
+# This is line 1981 of a file with a large header.
+# This is line 1982 of a file with a large header.
+# This is line 1983 of a file with a large header.
+# This is line 1984 of a file with a large header.
+# This is line 1985 of a file with a large header.
+# This is line 1986 of a file with a large header.
+# This is line 1987 of a file with a large header.
+# This is line 1988 of a file with a large header.
+# This is line 1989 of a file with a large header.
+# This is line 1990 of a file with a large header.
+# This is line 1991 of a file with a large header.
+# This is line 1992 of a file with a large header.
+# This is line 1993 of a file with a large header.
+# This is line 1994 of a file with a large header.
+# This is line 1995 of a file with a large header.
+# This is line 1996 of a file with a large header.
+# This is line 1997 of a file with a large header.
+# This is line 1998 of a file with a large header.
+# This is line 1999 of a file with a large header.
+# This is line 2000 of a file with a large header.
+# This is line 2001 of a file with a large header.
+# This is line 2002 of a file with a large header.
+# This is line 2003 of a file with a large header.
+# This is line 2004 of a file with a large header.
+# This is line 2005 of a file with a large header.
+# This is line 2006 of a file with a large header.
+# This is line 2007 of a file with a large header.
+# This is line 2008 of a file with a large header.
+# This is line 2009 of a file with a large header.
+# This is line 2010 of a file with a large header.
+# This is line 2011 of a file with a large header.
+# This is line 2012 of a file with a large header.
+# This is line 2013 of a file with a large header.
+# This is line 2014 of a file with a large header.
+# This is line 2015 of a file with a large header.
+# This is line 2016 of a file with a large header.
+# This is line 2017 of a file with a large header.
+# This is line 2018 of a file with a large header.
+# This is line 2019 of a file with a large header.
+# This is line 2020 of a file with a large header.
+# This is line 2021 of a file with a large header.
+# This is line 2022 of a file with a large header.
+# This is line 2023 of a file with a large header.
+# This is line 2024 of a file with a large header.
+# This is line 2025 of a file with a large header.
+# This is line 2026 of a file with a large header.
+# This is line 2027 of a file with a large header.
+# This is line 2028 of a file with a large header.
+# This is line 2029 of a file with a large header.
+# This is line 2030 of a file with a large header.
+# This is line 2031 of a file with a large header.
+# This is line 2032 of a file with a large header.
+# This is line 2033 of a file with a large header.
+# This is line 2034 of a file with a large header.
+# This is line 2035 of a file with a large header.
+# This is line 2036 of a file with a large header.
+# This is line 2037 of a file with a large header.
+# This is line 2038 of a file with a large header.
+# This is line 2039 of a file with a large header.
+# This is line 2040 of a file with a large header.
+# This is line 2041 of a file with a large header.
+# This is line 2042 of a file with a large header.
+# This is line 2043 of a file with a large header.
+# This is line 2044 of a file with a large header.
+# This is line 2045 of a file with a large header.
+# This is line 2046 of a file with a large header.
+# This is line 2047 of a file with a large header.
+# This is line 2048 of a file with a large header.
+# This is line 2049 of a file with a large header.
+# This is line 2050 of a file with a large header.
+# This is line 2051 of a file with a large header.
+# This is line 2052 of a file with a large header.
+# This is line 2053 of a file with a large header.
+# This is line 2054 of a file with a large header.
+# This is line 2055 of a file with a large header.
+# This is line 2056 of a file with a large header.
+# This is line 2057 of a file with a large header.
+# This is line 2058 of a file with a large header.
+# This is line 2059 of a file with a large header.
+# This is line 2060 of a file with a large header.
+# This is line 2061 of a file with a large header.
+# This is line 2062 of a file with a large header.
+# This is line 2063 of a file with a large header.
+# This is line 2064 of a file with a large header.
+# This is line 2065 of a file with a large header.
+# This is line 2066 of a file with a large header.
+# This is line 2067 of a file with a large header.
+# This is line 2068 of a file with a large header.
+# This is line 2069 of a file with a large header.
+# This is line 2070 of a file with a large header.
+# This is line 2071 of a file with a large header.
+# This is line 2072 of a file with a large header.
+# This is line 2073 of a file with a large header.
+# This is line 2074 of a file with a large header.
+# This is line 2075 of a file with a large header.
+# This is line 2076 of a file with a large header.
+# This is line 2077 of a file with a large header.
+# This is line 2078 of a file with a large header.
+# This is line 2079 of a file with a large header.
+# This is line 2080 of a file with a large header.
+# This is line 2081 of a file with a large header.
+# This is line 2082 of a file with a large header.
+# This is line 2083 of a file with a large header.
+# This is line 2084 of a file with a large header.
+# This is line 2085 of a file with a large header.
+# This is line 2086 of a file with a large header.
+# This is line 2087 of a file with a large header.
+# This is line 2088 of a file with a large header.
+# This is line 2089 of a file with a large header.
+# This is line 2090 of a file with a large header.
+# This is line 2091 of a file with a large header.
+# This is line 2092 of a file with a large header.
+# This is line 2093 of a file with a large header.
+# This is line 2094 of a file with a large header.
+# This is line 2095 of a file with a large header.
+# This is line 2096 of a file with a large header.
+# This is line 2097 of a file with a large header.
+# This is line 2098 of a file with a large header.
+# This is line 2099 of a file with a large header.
+# This is line 2100 of a file with a large header.
+# This is line 2101 of a file with a large header.
+# This is line 2102 of a file with a large header.
+# This is line 2103 of a file with a large header.
+# This is line 2104 of a file with a large header.
+# This is line 2105 of a file with a large header.
+# This is line 2106 of a file with a large header.
+# This is line 2107 of a file with a large header.
+# This is line 2108 of a file with a large header.
+# This is line 2109 of a file with a large header.
+# This is line 2110 of a file with a large header.
+# This is line 2111 of a file with a large header.
+# This is line 2112 of a file with a large header.
+# This is line 2113 of a file with a large header.
+# This is line 2114 of a file with a large header.
+# This is line 2115 of a file with a large header.
+# This is line 2116 of a file with a large header.
+# This is line 2117 of a file with a large header.
+# This is line 2118 of a file with a large header.
+# This is line 2119 of a file with a large header.
+# This is line 2120 of a file with a large header.
+# This is line 2121 of a file with a large header.
+# This is line 2122 of a file with a large header.
+# This is line 2123 of a file with a large header.
+# This is line 2124 of a file with a large header.
+# This is line 2125 of a file with a large header.
+# This is line 2126 of a file with a large header.
+# This is line 2127 of a file with a large header.
+# This is line 2128 of a file with a large header.
+# This is line 2129 of a file with a large header.
+# This is line 2130 of a file with a large header.
+# This is line 2131 of a file with a large header.
+# This is line 2132 of a file with a large header.
+# This is line 2133 of a file with a large header.
+# This is line 2134 of a file with a large header.
+# This is line 2135 of a file with a large header.
+# This is line 2136 of a file with a large header.
+# This is line 2137 of a file with a large header.
+# This is line 2138 of a file with a large header.
+# This is line 2139 of a file with a large header.
+# This is line 2140 of a file with a large header.
+# This is line 2141 of a file with a large header.
+# This is line 2142 of a file with a large header.
+# This is line 2143 of a file with a large header.
+# This is line 2144 of a file with a large header.
+# This is line 2145 of a file with a large header.
+# This is line 2146 of a file with a large header.
+# This is line 2147 of a file with a large header.
+# This is line 2148 of a file with a large header.
+# This is line 2149 of a file with a large header.
+# This is line 2150 of a file with a large header.
+# This is line 2151 of a file with a large header.
+# This is line 2152 of a file with a large header.
+# This is line 2153 of a file with a large header.
+# This is line 2154 of a file with a large header.
+# This is line 2155 of a file with a large header.
+# This is line 2156 of a file with a large header.
+# This is line 2157 of a file with a large header.
+# This is line 2158 of a file with a large header.
+# This is line 2159 of a file with a large header.
+# This is line 2160 of a file with a large header.
+# This is line 2161 of a file with a large header.
+# This is line 2162 of a file with a large header.
+# This is line 2163 of a file with a large header.
+# This is line 2164 of a file with a large header.
+# This is line 2165 of a file with a large header.
+# This is line 2166 of a file with a large header.
+# This is line 2167 of a file with a large header.
+# This is line 2168 of a file with a large header.
+# This is line 2169 of a file with a large header.
+# This is line 2170 of a file with a large header.
+# This is line 2171 of a file with a large header.
+# This is line 2172 of a file with a large header.
+# This is line 2173 of a file with a large header.
+# This is line 2174 of a file with a large header.
+# This is line 2175 of a file with a large header.
+# This is line 2176 of a file with a large header.
+# This is line 2177 of a file with a large header.
+# This is line 2178 of a file with a large header.
+# This is line 2179 of a file with a large header.
+# This is line 2180 of a file with a large header.
+# This is line 2181 of a file with a large header.
+# This is line 2182 of a file with a large header.
+# This is line 2183 of a file with a large header.
+# This is line 2184 of a file with a large header.
+# This is line 2185 of a file with a large header.
+# This is line 2186 of a file with a large header.
+# This is line 2187 of a file with a large header.
+# This is line 2188 of a file with a large header.
+# This is line 2189 of a file with a large header.
+# This is line 2190 of a file with a large header.
+# This is line 2191 of a file with a large header.
+# This is line 2192 of a file with a large header.
+# This is line 2193 of a file with a large header.
+# This is line 2194 of a file with a large header.
+# This is line 2195 of a file with a large header.
+# This is line 2196 of a file with a large header.
+# This is line 2197 of a file with a large header.
+# This is line 2198 of a file with a large header.
+# This is line 2199 of a file with a large header.
+# This is line 2200 of a file with a large header.
+# This is line 2201 of a file with a large header.
+# This is line 2202 of a file with a large header.
+# This is line 2203 of a file with a large header.
+# This is line 2204 of a file with a large header.
+# This is line 2205 of a file with a large header.
+# This is line 2206 of a file with a large header.
+# This is line 2207 of a file with a large header.
+# This is line 2208 of a file with a large header.
+# This is line 2209 of a file with a large header.
+# This is line 2210 of a file with a large header.
+# This is line 2211 of a file with a large header.
+# This is line 2212 of a file with a large header.
+# This is line 2213 of a file with a large header.
+# This is line 2214 of a file with a large header.
+# This is line 2215 of a file with a large header.
+# This is line 2216 of a file with a large header.
+# This is line 2217 of a file with a large header.
+# This is line 2218 of a file with a large header.
+# This is line 2219 of a file with a large header.
+# This is line 2220 of a file with a large header.
+# This is line 2221 of a file with a large header.
+# This is line 2222 of a file with a large header.
+# This is line 2223 of a file with a large header.
+# This is line 2224 of a file with a large header.
+# This is line 2225 of a file with a large header.
+# This is line 2226 of a file with a large header.
+# This is line 2227 of a file with a large header.
+# This is line 2228 of a file with a large header.
+# This is line 2229 of a file with a large header.
+# This is line 2230 of a file with a large header.
+# This is line 2231 of a file with a large header.
+# This is line 2232 of a file with a large header.
+# This is line 2233 of a file with a large header.
+# This is line 2234 of a file with a large header.
+# This is line 2235 of a file with a large header.
+# This is line 2236 of a file with a large header.
+# This is line 2237 of a file with a large header.
+# This is line 2238 of a file with a large header.
+# This is line 2239 of a file with a large header.
+# This is line 2240 of a file with a large header.
+# This is line 2241 of a file with a large header.
+# This is line 2242 of a file with a large header.
+# This is line 2243 of a file with a large header.
+# This is line 2244 of a file with a large header.
+# This is line 2245 of a file with a large header.
+# This is line 2246 of a file with a large header.
+# This is line 2247 of a file with a large header.
+# This is line 2248 of a file with a large header.
+# This is line 2249 of a file with a large header.
+# This is line 2250 of a file with a large header.
+# This is line 2251 of a file with a large header.
+# This is line 2252 of a file with a large header.
+# This is line 2253 of a file with a large header.
+# This is line 2254 of a file with a large header.
+# This is line 2255 of a file with a large header.
+# This is line 2256 of a file with a large header.
+# This is line 2257 of a file with a large header.
+# This is line 2258 of a file with a large header.
+# This is line 2259 of a file with a large header.
+# This is line 2260 of a file with a large header.
+# This is line 2261 of a file with a large header.
+# This is line 2262 of a file with a large header.
+# This is line 2263 of a file with a large header.
+# This is line 2264 of a file with a large header.
+# This is line 2265 of a file with a large header.
+# This is line 2266 of a file with a large header.
+# This is line 2267 of a file with a large header.
+# This is line 2268 of a file with a large header.
+# This is line 2269 of a file with a large header.
+# This is line 2270 of a file with a large header.
+# This is line 2271 of a file with a large header.
+# This is line 2272 of a file with a large header.
+# This is line 2273 of a file with a large header.
+# This is line 2274 of a file with a large header.
+# This is line 2275 of a file with a large header.
+# This is line 2276 of a file with a large header.
+# This is line 2277 of a file with a large header.
+# This is line 2278 of a file with a large header.
+# This is line 2279 of a file with a large header.
+# This is line 2280 of a file with a large header.
+# This is line 2281 of a file with a large header.
+# This is line 2282 of a file with a large header.
+# This is line 2283 of a file with a large header.
+# This is line 2284 of a file with a large header.
+# This is line 2285 of a file with a large header.
+# This is line 2286 of a file with a large header.
+# This is line 2287 of a file with a large header.
+# This is line 2288 of a file with a large header.
+# This is line 2289 of a file with a large header.
+# This is line 2290 of a file with a large header.
+# This is line 2291 of a file with a large header.
+# This is line 2292 of a file with a large header.
+# This is line 2293 of a file with a large header.
+# This is line 2294 of a file with a large header.
+# This is line 2295 of a file with a large header.
+# This is line 2296 of a file with a large header.
+# This is line 2297 of a file with a large header.
+# This is line 2298 of a file with a large header.
+# This is line 2299 of a file with a large header.
+# This is line 2300 of a file with a large header.
+# This is line 2301 of a file with a large header.
+# This is line 2302 of a file with a large header.
+# This is line 2303 of a file with a large header.
+# This is line 2304 of a file with a large header.
+# This is line 2305 of a file with a large header.
+# This is line 2306 of a file with a large header.
+# This is line 2307 of a file with a large header.
+# This is line 2308 of a file with a large header.
+# This is line 2309 of a file with a large header.
+# This is line 2310 of a file with a large header.
+# This is line 2311 of a file with a large header.
+# This is line 2312 of a file with a large header.
+# This is line 2313 of a file with a large header.
+# This is line 2314 of a file with a large header.
+# This is line 2315 of a file with a large header.
+# This is line 2316 of a file with a large header.
+# This is line 2317 of a file with a large header.
+# This is line 2318 of a file with a large header.
+# This is line 2319 of a file with a large header.
+# This is line 2320 of a file with a large header.
+# This is line 2321 of a file with a large header.
+# This is line 2322 of a file with a large header.
+# This is line 2323 of a file with a large header.
+# This is line 2324 of a file with a large header.
+# This is line 2325 of a file with a large header.
+# This is line 2326 of a file with a large header.
+# This is line 2327 of a file with a large header.
+# This is line 2328 of a file with a large header.
+# This is line 2329 of a file with a large header.
+# This is line 2330 of a file with a large header.
+# This is line 2331 of a file with a large header.
+# This is line 2332 of a file with a large header.
+# This is line 2333 of a file with a large header.
+# This is line 2334 of a file with a large header.
+# This is line 2335 of a file with a large header.
+# This is line 2336 of a file with a large header.
+# This is line 2337 of a file with a large header.
+# This is line 2338 of a file with a large header.
+# This is line 2339 of a file with a large header.
+# This is line 2340 of a file with a large header.
+# This is line 2341 of a file with a large header.
+# This is line 2342 of a file with a large header.
+# This is line 2343 of a file with a large header.
+# This is line 2344 of a file with a large header.
+# This is line 2345 of a file with a large header.
+# This is line 2346 of a file with a large header.
+# This is line 2347 of a file with a large header.
+# This is line 2348 of a file with a large header.
+# This is line 2349 of a file with a large header.
+# This is line 2350 of a file with a large header.
+# This is line 2351 of a file with a large header.
+# This is line 2352 of a file with a large header.
+# This is line 2353 of a file with a large header.
+# This is line 2354 of a file with a large header.
+# This is line 2355 of a file with a large header.
+# This is line 2356 of a file with a large header.
+# This is line 2357 of a file with a large header.
+# This is line 2358 of a file with a large header.
+# This is line 2359 of a file with a large header.
+# This is line 2360 of a file with a large header.
+# This is line 2361 of a file with a large header.
+# This is line 2362 of a file with a large header.
+# This is line 2363 of a file with a large header.
+# This is line 2364 of a file with a large header.
+# This is line 2365 of a file with a large header.
+# This is line 2366 of a file with a large header.
+# This is line 2367 of a file with a large header.
+# This is line 2368 of a file with a large header.
+# This is line 2369 of a file with a large header.
+# This is line 2370 of a file with a large header.
+# This is line 2371 of a file with a large header.
+# This is line 2372 of a file with a large header.
+# This is line 2373 of a file with a large header.
+# This is line 2374 of a file with a large header.
+# This is line 2375 of a file with a large header.
+# This is line 2376 of a file with a large header.
+# This is line 2377 of a file with a large header.
+# This is line 2378 of a file with a large header.
+# This is line 2379 of a file with a large header.
+# This is line 2380 of a file with a large header.
+# This is line 2381 of a file with a large header.
+# This is line 2382 of a file with a large header.
+# This is line 2383 of a file with a large header.
+# This is line 2384 of a file with a large header.
+# This is line 2385 of a file with a large header.
+# This is line 2386 of a file with a large header.
+# This is line 2387 of a file with a large header.
+# This is line 2388 of a file with a large header.
+# This is line 2389 of a file with a large header.
+# This is line 2390 of a file with a large header.
+# This is line 2391 of a file with a large header.
+# This is line 2392 of a file with a large header.
+# This is line 2393 of a file with a large header.
+# This is line 2394 of a file with a large header.
+# This is line 2395 of a file with a large header.
+# This is line 2396 of a file with a large header.
+# This is line 2397 of a file with a large header.
+# This is line 2398 of a file with a large header.
+# This is line 2399 of a file with a large header.
+# This is line 2400 of a file with a large header.
+# This is line 2401 of a file with a large header.
+# This is line 2402 of a file with a large header.
+# This is line 2403 of a file with a large header.
+# This is line 2404 of a file with a large header.
+# This is line 2405 of a file with a large header.
+# This is line 2406 of a file with a large header.
+# This is line 2407 of a file with a large header.
+# This is line 2408 of a file with a large header.
+# This is line 2409 of a file with a large header.
+# This is line 2410 of a file with a large header.
+# This is line 2411 of a file with a large header.
+# This is line 2412 of a file with a large header.
+# This is line 2413 of a file with a large header.
+# This is line 2414 of a file with a large header.
+# This is line 2415 of a file with a large header.
+# This is line 2416 of a file with a large header.
+# This is line 2417 of a file with a large header.
+# This is line 2418 of a file with a large header.
+# This is line 2419 of a file with a large header.
+# This is line 2420 of a file with a large header.
+# This is line 2421 of a file with a large header.
+# This is line 2422 of a file with a large header.
+# This is line 2423 of a file with a large header.
+# This is line 2424 of a file with a large header.
+# This is line 2425 of a file with a large header.
+# This is line 2426 of a file with a large header.
+# This is line 2427 of a file with a large header.
+# This is line 2428 of a file with a large header.
+# This is line 2429 of a file with a large header.
+# This is line 2430 of a file with a large header.
+# This is line 2431 of a file with a large header.
+# This is line 2432 of a file with a large header.
+# This is line 2433 of a file with a large header.
+# This is line 2434 of a file with a large header.
+# This is line 2435 of a file with a large header.
+# This is line 2436 of a file with a large header.
+# This is line 2437 of a file with a large header.
+# This is line 2438 of a file with a large header.
+# This is line 2439 of a file with a large header.
+# This is line 2440 of a file with a large header.
+# This is line 2441 of a file with a large header.
+# This is line 2442 of a file with a large header.
+# This is line 2443 of a file with a large header.
+# This is line 2444 of a file with a large header.
+# This is line 2445 of a file with a large header.
+# This is line 2446 of a file with a large header.
+# This is line 2447 of a file with a large header.
+# This is line 2448 of a file with a large header.
+# This is line 2449 of a file with a large header.
+# This is line 2450 of a file with a large header.
+# This is line 2451 of a file with a large header.
+# This is line 2452 of a file with a large header.
+# This is line 2453 of a file with a large header.
+# This is line 2454 of a file with a large header.
+# This is line 2455 of a file with a large header.
+# This is line 2456 of a file with a large header.
+# This is line 2457 of a file with a large header.
+# This is line 2458 of a file with a large header.
+# This is line 2459 of a file with a large header.
+# This is line 2460 of a file with a large header.
+# This is line 2461 of a file with a large header.
+# This is line 2462 of a file with a large header.
+# This is line 2463 of a file with a large header.
+# This is line 2464 of a file with a large header.
+# This is line 2465 of a file with a large header.
+# This is line 2466 of a file with a large header.
+# This is line 2467 of a file with a large header.
+# This is line 2468 of a file with a large header.
+# This is line 2469 of a file with a large header.
+# This is line 2470 of a file with a large header.
+# This is line 2471 of a file with a large header.
+# This is line 2472 of a file with a large header.
+# This is line 2473 of a file with a large header.
+# This is line 2474 of a file with a large header.
+# This is line 2475 of a file with a large header.
+# This is line 2476 of a file with a large header.
+# This is line 2477 of a file with a large header.
+# This is line 2478 of a file with a large header.
+# This is line 2479 of a file with a large header.
+# This is line 2480 of a file with a large header.
+# This is line 2481 of a file with a large header.
+# This is line 2482 of a file with a large header.
+# This is line 2483 of a file with a large header.
+# This is line 2484 of a file with a large header.
+# This is line 2485 of a file with a large header.
+# This is line 2486 of a file with a large header.
+# This is line 2487 of a file with a large header.
+# This is line 2488 of a file with a large header.
+# This is line 2489 of a file with a large header.
+# This is line 2490 of a file with a large header.
+# This is line 2491 of a file with a large header.
+# This is line 2492 of a file with a large header.
+# This is line 2493 of a file with a large header.
+# This is line 2494 of a file with a large header.
+# This is line 2495 of a file with a large header.
+# This is line 2496 of a file with a large header.
+# This is line 2497 of a file with a large header.
+# This is line 2498 of a file with a large header.
+# This is line 2499 of a file with a large header.
+# This is line 2500 of a file with a large header.
+# This is line 2501 of a file with a large header.
+# This is line 2502 of a file with a large header.
+# This is line 2503 of a file with a large header.
+# This is line 2504 of a file with a large header.
+# This is line 2505 of a file with a large header.
+# This is line 2506 of a file with a large header.
+# This is line 2507 of a file with a large header.
+# This is line 2508 of a file with a large header.
+# This is line 2509 of a file with a large header.
+# This is line 2510 of a file with a large header.
+# This is line 2511 of a file with a large header.
+# This is line 2512 of a file with a large header.
+# This is line 2513 of a file with a large header.
+# This is line 2514 of a file with a large header.
+# This is line 2515 of a file with a large header.
+# This is line 2516 of a file with a large header.
+# This is line 2517 of a file with a large header.
+# This is line 2518 of a file with a large header.
+# This is line 2519 of a file with a large header.
+# This is line 2520 of a file with a large header.
+# This is line 2521 of a file with a large header.
+# This is line 2522 of a file with a large header.
+# This is line 2523 of a file with a large header.
+# This is line 2524 of a file with a large header.
+# This is line 2525 of a file with a large header.
+# This is line 2526 of a file with a large header.
+# This is line 2527 of a file with a large header.
+# This is line 2528 of a file with a large header.
+# This is line 2529 of a file with a large header.
+# This is line 2530 of a file with a large header.
+# This is line 2531 of a file with a large header.
+# This is line 2532 of a file with a large header.
+# This is line 2533 of a file with a large header.
+# This is line 2534 of a file with a large header.
+# This is line 2535 of a file with a large header.
+# This is line 2536 of a file with a large header.
+# This is line 2537 of a file with a large header.
+# This is line 2538 of a file with a large header.
+# This is line 2539 of a file with a large header.
+# This is line 2540 of a file with a large header.
+# This is line 2541 of a file with a large header.
+# This is line 2542 of a file with a large header.
+# This is line 2543 of a file with a large header.
+# This is line 2544 of a file with a large header.
+# This is line 2545 of a file with a large header.
+# This is line 2546 of a file with a large header.
+# This is line 2547 of a file with a large header.
+# This is line 2548 of a file with a large header.
+# This is line 2549 of a file with a large header.
+# This is line 2550 of a file with a large header.
+# This is line 2551 of a file with a large header.
+# This is line 2552 of a file with a large header.
+# This is line 2553 of a file with a large header.
+# This is line 2554 of a file with a large header.
+# This is line 2555 of a file with a large header.
+# This is line 2556 of a file with a large header.
+# This is line 2557 of a file with a large header.
+# This is line 2558 of a file with a large header.
+# This is line 2559 of a file with a large header.
+# This is line 2560 of a file with a large header.
+# This is line 2561 of a file with a large header.
+# This is line 2562 of a file with a large header.
+# This is line 2563 of a file with a large header.
+# This is line 2564 of a file with a large header.
+# This is line 2565 of a file with a large header.
+# This is line 2566 of a file with a large header.
+# This is line 2567 of a file with a large header.
+# This is line 2568 of a file with a large header.
+# This is line 2569 of a file with a large header.
+# This is line 2570 of a file with a large header.
+# This is line 2571 of a file with a large header.
+# This is line 2572 of a file with a large header.
+# This is line 2573 of a file with a large header.
+# This is line 2574 of a file with a large header.
+# This is line 2575 of a file with a large header.
+# This is line 2576 of a file with a large header.
+# This is line 2577 of a file with a large header.
+# This is line 2578 of a file with a large header.
+# This is line 2579 of a file with a large header.
+# This is line 2580 of a file with a large header.
+# This is line 2581 of a file with a large header.
+# This is line 2582 of a file with a large header.
+# This is line 2583 of a file with a large header.
+# This is line 2584 of a file with a large header.
+# This is line 2585 of a file with a large header.
+# This is line 2586 of a file with a large header.
+# This is line 2587 of a file with a large header.
+# This is line 2588 of a file with a large header.
+# This is line 2589 of a file with a large header.
+# This is line 2590 of a file with a large header.
+# This is line 2591 of a file with a large header.
+# This is line 2592 of a file with a large header.
+# This is line 2593 of a file with a large header.
+# This is line 2594 of a file with a large header.
+# This is line 2595 of a file with a large header.
+# This is line 2596 of a file with a large header.
+# This is line 2597 of a file with a large header.
+# This is line 2598 of a file with a large header.
+# This is line 2599 of a file with a large header.
+# This is line 2600 of a file with a large header.
+# This is line 2601 of a file with a large header.
+# This is line 2602 of a file with a large header.
+# This is line 2603 of a file with a large header.
+# This is line 2604 of a file with a large header.
+# This is line 2605 of a file with a large header.
+# This is line 2606 of a file with a large header.
+# This is line 2607 of a file with a large header.
+# This is line 2608 of a file with a large header.
+# This is line 2609 of a file with a large header.
+# This is line 2610 of a file with a large header.
+# This is line 2611 of a file with a large header.
+# This is line 2612 of a file with a large header.
+# This is line 2613 of a file with a large header.
+# This is line 2614 of a file with a large header.
+# This is line 2615 of a file with a large header.
+# This is line 2616 of a file with a large header.
+# This is line 2617 of a file with a large header.
+# This is line 2618 of a file with a large header.
+# This is line 2619 of a file with a large header.
+# This is line 2620 of a file with a large header.
+# This is line 2621 of a file with a large header.
+# This is line 2622 of a file with a large header.
+# This is line 2623 of a file with a large header.
+# This is line 2624 of a file with a large header.
+# This is line 2625 of a file with a large header.
+# This is line 2626 of a file with a large header.
+# This is line 2627 of a file with a large header.
+# This is line 2628 of a file with a large header.
+# This is line 2629 of a file with a large header.
+# This is line 2630 of a file with a large header.
+# This is line 2631 of a file with a large header.
+# This is line 2632 of a file with a large header.
+# This is line 2633 of a file with a large header.
+# This is line 2634 of a file with a large header.
+# This is line 2635 of a file with a large header.
+# This is line 2636 of a file with a large header.
+# This is line 2637 of a file with a large header.
+# This is line 2638 of a file with a large header.
+# This is line 2639 of a file with a large header.
+# This is line 2640 of a file with a large header.
+# This is line 2641 of a file with a large header.
+# This is line 2642 of a file with a large header.
+# This is line 2643 of a file with a large header.
+# This is line 2644 of a file with a large header.
+# This is line 2645 of a file with a large header.
+# This is line 2646 of a file with a large header.
+# This is line 2647 of a file with a large header.
+# This is line 2648 of a file with a large header.
+# This is line 2649 of a file with a large header.
+# This is line 2650 of a file with a large header.
+# This is line 2651 of a file with a large header.
+# This is line 2652 of a file with a large header.
+# This is line 2653 of a file with a large header.
+# This is line 2654 of a file with a large header.
+# This is line 2655 of a file with a large header.
+# This is line 2656 of a file with a large header.
+# This is line 2657 of a file with a large header.
+# This is line 2658 of a file with a large header.
+# This is line 2659 of a file with a large header.
+# This is line 2660 of a file with a large header.
+# This is line 2661 of a file with a large header.
+# This is line 2662 of a file with a large header.
+# This is line 2663 of a file with a large header.
+# This is line 2664 of a file with a large header.
+# This is line 2665 of a file with a large header.
+# This is line 2666 of a file with a large header.
+# This is line 2667 of a file with a large header.
+# This is line 2668 of a file with a large header.
+# This is line 2669 of a file with a large header.
+# This is line 2670 of a file with a large header.
+# This is line 2671 of a file with a large header.
+# This is line 2672 of a file with a large header.
+# This is line 2673 of a file with a large header.
+# This is line 2674 of a file with a large header.
+# This is line 2675 of a file with a large header.
+# This is line 2676 of a file with a large header.
+# This is line 2677 of a file with a large header.
+# This is line 2678 of a file with a large header.
+# This is line 2679 of a file with a large header.
+# This is line 2680 of a file with a large header.
+# This is line 2681 of a file with a large header.
+# This is line 2682 of a file with a large header.
+# This is line 2683 of a file with a large header.
+# This is line 2684 of a file with a large header.
+# This is line 2685 of a file with a large header.
+# This is line 2686 of a file with a large header.
+# This is line 2687 of a file with a large header.
+# This is line 2688 of a file with a large header.
+# This is line 2689 of a file with a large header.
+# This is line 2690 of a file with a large header.
+# This is line 2691 of a file with a large header.
+# This is line 2692 of a file with a large header.
+# This is line 2693 of a file with a large header.
+# This is line 2694 of a file with a large header.
+# This is line 2695 of a file with a large header.
+# This is line 2696 of a file with a large header.
+# This is line 2697 of a file with a large header.
+# This is line 2698 of a file with a large header.
+# This is line 2699 of a file with a large header.
+# This is line 2700 of a file with a large header.
+# This is line 2701 of a file with a large header.
+# This is line 2702 of a file with a large header.
+# This is line 2703 of a file with a large header.
+# This is line 2704 of a file with a large header.
+# This is line 2705 of a file with a large header.
+# This is line 2706 of a file with a large header.
+# This is line 2707 of a file with a large header.
+# This is line 2708 of a file with a large header.
+# This is line 2709 of a file with a large header.
+# This is line 2710 of a file with a large header.
+# This is line 2711 of a file with a large header.
+# This is line 2712 of a file with a large header.
+# This is line 2713 of a file with a large header.
+# This is line 2714 of a file with a large header.
+# This is line 2715 of a file with a large header.
+# This is line 2716 of a file with a large header.
+# This is line 2717 of a file with a large header.
+# This is line 2718 of a file with a large header.
+# This is line 2719 of a file with a large header.
+# This is line 2720 of a file with a large header.
+# This is line 2721 of a file with a large header.
+# This is line 2722 of a file with a large header.
+# This is line 2723 of a file with a large header.
+# This is line 2724 of a file with a large header.
+# This is line 2725 of a file with a large header.
+# This is line 2726 of a file with a large header.
+# This is line 2727 of a file with a large header.
+# This is line 2728 of a file with a large header.
+# This is line 2729 of a file with a large header.
+# This is line 2730 of a file with a large header.
+# This is line 2731 of a file with a large header.
+# This is line 2732 of a file with a large header.
+# This is line 2733 of a file with a large header.
+# This is line 2734 of a file with a large header.
+# This is line 2735 of a file with a large header.
+# This is line 2736 of a file with a large header.
+# This is line 2737 of a file with a large header.
+# This is line 2738 of a file with a large header.
+# This is line 2739 of a file with a large header.
+# This is line 2740 of a file with a large header.
+# This is line 2741 of a file with a large header.
+# This is line 2742 of a file with a large header.
+# This is line 2743 of a file with a large header.
+# This is line 2744 of a file with a large header.
+# This is line 2745 of a file with a large header.
+# This is line 2746 of a file with a large header.
+# This is line 2747 of a file with a large header.
+# This is line 2748 of a file with a large header.
+# This is line 2749 of a file with a large header.
+# This is line 2750 of a file with a large header.
+# This is line 2751 of a file with a large header.
+# This is line 2752 of a file with a large header.
+# This is line 2753 of a file with a large header.
+# This is line 2754 of a file with a large header.
+# This is line 2755 of a file with a large header.
+# This is line 2756 of a file with a large header.
+# This is line 2757 of a file with a large header.
+# This is line 2758 of a file with a large header.
+# This is line 2759 of a file with a large header.
+# This is line 2760 of a file with a large header.
+# This is line 2761 of a file with a large header.
+# This is line 2762 of a file with a large header.
+# This is line 2763 of a file with a large header.
+# This is line 2764 of a file with a large header.
+# This is line 2765 of a file with a large header.
+# This is line 2766 of a file with a large header.
+# This is line 2767 of a file with a large header.
+# This is line 2768 of a file with a large header.
+# This is line 2769 of a file with a large header.
+# This is line 2770 of a file with a large header.
+# This is line 2771 of a file with a large header.
+# This is line 2772 of a file with a large header.
+# This is line 2773 of a file with a large header.
+# This is line 2774 of a file with a large header.
+# This is line 2775 of a file with a large header.
+# This is line 2776 of a file with a large header.
+# This is line 2777 of a file with a large header.
+# This is line 2778 of a file with a large header.
+# This is line 2779 of a file with a large header.
+# This is line 2780 of a file with a large header.
+# This is line 2781 of a file with a large header.
+# This is line 2782 of a file with a large header.
+# This is line 2783 of a file with a large header.
+# This is line 2784 of a file with a large header.
+# This is line 2785 of a file with a large header.
+# This is line 2786 of a file with a large header.
+# This is line 2787 of a file with a large header.
+# This is line 2788 of a file with a large header.
+# This is line 2789 of a file with a large header.
+# This is line 2790 of a file with a large header.
+# This is line 2791 of a file with a large header.
+# This is line 2792 of a file with a large header.
+# This is line 2793 of a file with a large header.
+# This is line 2794 of a file with a large header.
+# This is line 2795 of a file with a large header.
+# This is line 2796 of a file with a large header.
+# This is line 2797 of a file with a large header.
+# This is line 2798 of a file with a large header.
+# This is line 2799 of a file with a large header.
+# This is line 2800 of a file with a large header.
+# This is line 2801 of a file with a large header.
+# This is line 2802 of a file with a large header.
+# This is line 2803 of a file with a large header.
+# This is line 2804 of a file with a large header.
+# This is line 2805 of a file with a large header.
+# This is line 2806 of a file with a large header.
+# This is line 2807 of a file with a large header.
+# This is line 2808 of a file with a large header.
+# This is line 2809 of a file with a large header.
+# This is line 2810 of a file with a large header.
+# This is line 2811 of a file with a large header.
+# This is line 2812 of a file with a large header.
+# This is line 2813 of a file with a large header.
+# This is line 2814 of a file with a large header.
+# This is line 2815 of a file with a large header.
+# This is line 2816 of a file with a large header.
+# This is line 2817 of a file with a large header.
+# This is line 2818 of a file with a large header.
+# This is line 2819 of a file with a large header.
+# This is line 2820 of a file with a large header.
+# This is line 2821 of a file with a large header.
+# This is line 2822 of a file with a large header.
+# This is line 2823 of a file with a large header.
+# This is line 2824 of a file with a large header.
+# This is line 2825 of a file with a large header.
+# This is line 2826 of a file with a large header.
+# This is line 2827 of a file with a large header.
+# This is line 2828 of a file with a large header.
+# This is line 2829 of a file with a large header.
+# This is line 2830 of a file with a large header.
+# This is line 2831 of a file with a large header.
+# This is line 2832 of a file with a large header.
+# This is line 2833 of a file with a large header.
+# This is line 2834 of a file with a large header.
+# This is line 2835 of a file with a large header.
+# This is line 2836 of a file with a large header.
+# This is line 2837 of a file with a large header.
+# This is line 2838 of a file with a large header.
+# This is line 2839 of a file with a large header.
+# This is line 2840 of a file with a large header.
+# This is line 2841 of a file with a large header.
+# This is line 2842 of a file with a large header.
+# This is line 2843 of a file with a large header.
+# This is line 2844 of a file with a large header.
+# This is line 2845 of a file with a large header.
+# This is line 2846 of a file with a large header.
+# This is line 2847 of a file with a large header.
+# This is line 2848 of a file with a large header.
+# This is line 2849 of a file with a large header.
+# This is line 2850 of a file with a large header.
+# This is line 2851 of a file with a large header.
+# This is line 2852 of a file with a large header.
+# This is line 2853 of a file with a large header.
+# This is line 2854 of a file with a large header.
+# This is line 2855 of a file with a large header.
+# This is line 2856 of a file with a large header.
+# This is line 2857 of a file with a large header.
+# This is line 2858 of a file with a large header.
+# This is line 2859 of a file with a large header.
+# This is line 2860 of a file with a large header.
+# This is line 2861 of a file with a large header.
+# This is line 2862 of a file with a large header.
+# This is line 2863 of a file with a large header.
+# This is line 2864 of a file with a large header.
+# This is line 2865 of a file with a large header.
+# This is line 2866 of a file with a large header.
+# This is line 2867 of a file with a large header.
+# This is line 2868 of a file with a large header.
+# This is line 2869 of a file with a large header.
+# This is line 2870 of a file with a large header.
+# This is line 2871 of a file with a large header.
+# This is line 2872 of a file with a large header.
+# This is line 2873 of a file with a large header.
+# This is line 2874 of a file with a large header.
+# This is line 2875 of a file with a large header.
+# This is line 2876 of a file with a large header.
+# This is line 2877 of a file with a large header.
+# This is line 2878 of a file with a large header.
+# This is line 2879 of a file with a large header.
+# This is line 2880 of a file with a large header.
+# This is line 2881 of a file with a large header.
+# This is line 2882 of a file with a large header.
+# This is line 2883 of a file with a large header.
+# This is line 2884 of a file with a large header.
+# This is line 2885 of a file with a large header.
+# This is line 2886 of a file with a large header.
+# This is line 2887 of a file with a large header.
+# This is line 2888 of a file with a large header.
+# This is line 2889 of a file with a large header.
+# This is line 2890 of a file with a large header.
+# This is line 2891 of a file with a large header.
+# This is line 2892 of a file with a large header.
+# This is line 2893 of a file with a large header.
+# This is line 2894 of a file with a large header.
+# This is line 2895 of a file with a large header.
+# This is line 2896 of a file with a large header.
+# This is line 2897 of a file with a large header.
+# This is line 2898 of a file with a large header.
+# This is line 2899 of a file with a large header.
+# This is line 2900 of a file with a large header.
+# This is line 2901 of a file with a large header.
+# This is line 2902 of a file with a large header.
+# This is line 2903 of a file with a large header.
+# This is line 2904 of a file with a large header.
+# This is line 2905 of a file with a large header.
+# This is line 2906 of a file with a large header.
+# This is line 2907 of a file with a large header.
+# This is line 2908 of a file with a large header.
+# This is line 2909 of a file with a large header.
+# This is line 2910 of a file with a large header.
+# This is line 2911 of a file with a large header.
+# This is line 2912 of a file with a large header.
+# This is line 2913 of a file with a large header.
+# This is line 2914 of a file with a large header.
+# This is line 2915 of a file with a large header.
+# This is line 2916 of a file with a large header.
+# This is line 2917 of a file with a large header.
+# This is line 2918 of a file with a large header.
+# This is line 2919 of a file with a large header.
+# This is line 2920 of a file with a large header.
+# This is line 2921 of a file with a large header.
+# This is line 2922 of a file with a large header.
+# This is line 2923 of a file with a large header.
+# This is line 2924 of a file with a large header.
+# This is line 2925 of a file with a large header.
+# This is line 2926 of a file with a large header.
+# This is line 2927 of a file with a large header.
+# This is line 2928 of a file with a large header.
+# This is line 2929 of a file with a large header.
+# This is line 2930 of a file with a large header.
+# This is line 2931 of a file with a large header.
+# This is line 2932 of a file with a large header.
+# This is line 2933 of a file with a large header.
+# This is line 2934 of a file with a large header.
+# This is line 2935 of a file with a large header.
+# This is line 2936 of a file with a large header.
+# This is line 2937 of a file with a large header.
+# This is line 2938 of a file with a large header.
+# This is line 2939 of a file with a large header.
+# This is line 2940 of a file with a large header.
+# This is line 2941 of a file with a large header.
+# This is line 2942 of a file with a large header.
+# This is line 2943 of a file with a large header.
+# This is line 2944 of a file with a large header.
+# This is line 2945 of a file with a large header.
+# This is line 2946 of a file with a large header.
+# This is line 2947 of a file with a large header.
+# This is line 2948 of a file with a large header.
+# This is line 2949 of a file with a large header.
+# This is line 2950 of a file with a large header.
+# This is line 2951 of a file with a large header.
+# This is line 2952 of a file with a large header.
+# This is line 2953 of a file with a large header.
+# This is line 2954 of a file with a large header.
+# This is line 2955 of a file with a large header.
+# This is line 2956 of a file with a large header.
+# This is line 2957 of a file with a large header.
+# This is line 2958 of a file with a large header.
+# This is line 2959 of a file with a large header.
+# This is line 2960 of a file with a large header.
+# This is line 2961 of a file with a large header.
+# This is line 2962 of a file with a large header.
+# This is line 2963 of a file with a large header.
+# This is line 2964 of a file with a large header.
+# This is line 2965 of a file with a large header.
+# This is line 2966 of a file with a large header.
+# This is line 2967 of a file with a large header.
+# This is line 2968 of a file with a large header.
+# This is line 2969 of a file with a large header.
+# This is line 2970 of a file with a large header.
+# This is line 2971 of a file with a large header.
+# This is line 2972 of a file with a large header.
+# This is line 2973 of a file with a large header.
+# This is line 2974 of a file with a large header.
+# This is line 2975 of a file with a large header.
+# This is line 2976 of a file with a large header.
+# This is line 2977 of a file with a large header.
+# This is line 2978 of a file with a large header.
+# This is line 2979 of a file with a large header.
+# This is line 2980 of a file with a large header.
+# This is line 2981 of a file with a large header.
+# This is line 2982 of a file with a large header.
+# This is line 2983 of a file with a large header.
+# This is line 2984 of a file with a large header.
+# This is line 2985 of a file with a large header.
+# This is line 2986 of a file with a large header.
+# This is line 2987 of a file with a large header.
+# This is line 2988 of a file with a large header.
+# This is line 2989 of a file with a large header.
+# This is line 2990 of a file with a large header.
+# This is line 2991 of a file with a large header.
+# This is line 2992 of a file with a large header.
+# This is line 2993 of a file with a large header.
+# This is line 2994 of a file with a large header.
+# This is line 2995 of a file with a large header.
+# This is line 2996 of a file with a large header.
+# This is line 2997 of a file with a large header.
+# This is line 2998 of a file with a large header.
+# This is line 2999 of a file with a large header.
+# This is line 3000 of a file with a large header.
+# This is line 3001 of a file with a large header.
+# This is line 3002 of a file with a large header.
+# This is line 3003 of a file with a large header.
+# This is line 3004 of a file with a large header.
+# This is line 3005 of a file with a large header.
+# This is line 3006 of a file with a large header.
+# This is line 3007 of a file with a large header.
+# This is line 3008 of a file with a large header.
+# This is line 3009 of a file with a large header.
+# This is line 3010 of a file with a large header.
+# This is line 3011 of a file with a large header.
+# This is line 3012 of a file with a large header.
+# This is line 3013 of a file with a large header.
+# This is line 3014 of a file with a large header.
+# This is line 3015 of a file with a large header.
+# This is line 3016 of a file with a large header.
+# This is line 3017 of a file with a large header.
+# This is line 3018 of a file with a large header.
+# This is line 3019 of a file with a large header.
+# This is line 3020 of a file with a large header.
+# This is line 3021 of a file with a large header.
+# This is line 3022 of a file with a large header.
+# This is line 3023 of a file with a large header.
+# This is line 3024 of a file with a large header.
+# This is line 3025 of a file with a large header.
+# This is line 3026 of a file with a large header.
+# This is line 3027 of a file with a large header.
+# This is line 3028 of a file with a large header.
+# This is line 3029 of a file with a large header.
+# This is line 3030 of a file with a large header.
+# This is line 3031 of a file with a large header.
+# This is line 3032 of a file with a large header.
+# This is line 3033 of a file with a large header.
+# This is line 3034 of a file with a large header.
+# This is line 3035 of a file with a large header.
+# This is line 3036 of a file with a large header.
+# This is line 3037 of a file with a large header.
+# This is line 3038 of a file with a large header.
+# This is line 3039 of a file with a large header.
+# This is line 3040 of a file with a large header.
+# This is line 3041 of a file with a large header.
+# This is line 3042 of a file with a large header.
+# This is line 3043 of a file with a large header.
+# This is line 3044 of a file with a large header.
+# This is line 3045 of a file with a large header.
+# This is line 3046 of a file with a large header.
+# This is line 3047 of a file with a large header.
+# This is line 3048 of a file with a large header.
+# This is line 3049 of a file with a large header.
+# This is line 3050 of a file with a large header.
+# This is line 3051 of a file with a large header.
+# This is line 3052 of a file with a large header.
+# This is line 3053 of a file with a large header.
+# This is line 3054 of a file with a large header.
+# This is line 3055 of a file with a large header.
+# This is line 3056 of a file with a large header.
+# This is line 3057 of a file with a large header.
+# This is line 3058 of a file with a large header.
+# This is line 3059 of a file with a large header.
+# This is line 3060 of a file with a large header.
+# This is line 3061 of a file with a large header.
+# This is line 3062 of a file with a large header.
+# This is line 3063 of a file with a large header.
+# This is line 3064 of a file with a large header.
+# This is line 3065 of a file with a large header.
+# This is line 3066 of a file with a large header.
+# This is line 3067 of a file with a large header.
+# This is line 3068 of a file with a large header.
+# This is line 3069 of a file with a large header.
+# This is line 3070 of a file with a large header.
+# This is line 3071 of a file with a large header.
+# This is line 3072 of a file with a large header.
+# This is line 3073 of a file with a large header.
+# This is line 3074 of a file with a large header.
+# This is line 3075 of a file with a large header.
+# This is line 3076 of a file with a large header.
+# This is line 3077 of a file with a large header.
+# This is line 3078 of a file with a large header.
+# This is line 3079 of a file with a large header.
+# This is line 3080 of a file with a large header.
+# This is line 3081 of a file with a large header.
+# This is line 3082 of a file with a large header.
+# This is line 3083 of a file with a large header.
+# This is line 3084 of a file with a large header.
+# This is line 3085 of a file with a large header.
+# This is line 3086 of a file with a large header.
+# This is line 3087 of a file with a large header.
+# This is line 3088 of a file with a large header.
+# This is line 3089 of a file with a large header.
+# This is line 3090 of a file with a large header.
+# This is line 3091 of a file with a large header.
+# This is line 3092 of a file with a large header.
+# This is line 3093 of a file with a large header.
+# This is line 3094 of a file with a large header.
+# This is line 3095 of a file with a large header.
+# This is line 3096 of a file with a large header.
+# This is line 3097 of a file with a large header.
+# This is line 3098 of a file with a large header.
+# This is line 3099 of a file with a large header.
+# This is line 3100 of a file with a large header.
+# This is line 3101 of a file with a large header.
+# This is line 3102 of a file with a large header.
+# This is line 3103 of a file with a large header.
+# This is line 3104 of a file with a large header.
+# This is line 3105 of a file with a large header.
+# This is line 3106 of a file with a large header.
+# This is line 3107 of a file with a large header.
+# This is line 3108 of a file with a large header.
+# This is line 3109 of a file with a large header.
+# This is line 3110 of a file with a large header.
+# This is line 3111 of a file with a large header.
+# This is line 3112 of a file with a large header.
+# This is line 3113 of a file with a large header.
+# This is line 3114 of a file with a large header.
+# This is line 3115 of a file with a large header.
+# This is line 3116 of a file with a large header.
+# This is line 3117 of a file with a large header.
+# This is line 3118 of a file with a large header.
+# This is line 3119 of a file with a large header.
+# This is line 3120 of a file with a large header.
+# This is line 3121 of a file with a large header.
+# This is line 3122 of a file with a large header.
+# This is line 3123 of a file with a large header.
+# This is line 3124 of a file with a large header.
+# This is line 3125 of a file with a large header.
+# This is line 3126 of a file with a large header.
+# This is line 3127 of a file with a large header.
+# This is line 3128 of a file with a large header.
+# This is line 3129 of a file with a large header.
+# This is line 3130 of a file with a large header.
+# This is line 3131 of a file with a large header.
+# This is line 3132 of a file with a large header.
+# This is line 3133 of a file with a large header.
+# This is line 3134 of a file with a large header.
+# This is line 3135 of a file with a large header.
+# This is line 3136 of a file with a large header.
+# This is line 3137 of a file with a large header.
+# This is line 3138 of a file with a large header.
+# This is line 3139 of a file with a large header.
+# This is line 3140 of a file with a large header.
+# This is line 3141 of a file with a large header.
+# This is line 3142 of a file with a large header.
+# This is line 3143 of a file with a large header.
+# This is line 3144 of a file with a large header.
+# This is line 3145 of a file with a large header.
+# This is line 3146 of a file with a large header.
+# This is line 3147 of a file with a large header.
+# This is line 3148 of a file with a large header.
+# This is line 3149 of a file with a large header.
+# This is line 3150 of a file with a large header.
+# This is line 3151 of a file with a large header.
+# This is line 3152 of a file with a large header.
+# This is line 3153 of a file with a large header.
+# This is line 3154 of a file with a large header.
+# This is line 3155 of a file with a large header.
+# This is line 3156 of a file with a large header.
+# This is line 3157 of a file with a large header.
+# This is line 3158 of a file with a large header.
+# This is line 3159 of a file with a large header.
+# This is line 3160 of a file with a large header.
+# This is line 3161 of a file with a large header.
+# This is line 3162 of a file with a large header.
+# This is line 3163 of a file with a large header.
+# This is line 3164 of a file with a large header.
+# This is line 3165 of a file with a large header.
+# This is line 3166 of a file with a large header.
+# This is line 3167 of a file with a large header.
+# This is line 3168 of a file with a large header.
+# This is line 3169 of a file with a large header.
+# This is line 3170 of a file with a large header.
+# This is line 3171 of a file with a large header.
+# This is line 3172 of a file with a large header.
+# This is line 3173 of a file with a large header.
+# This is line 3174 of a file with a large header.
+# This is line 3175 of a file with a large header.
+# This is line 3176 of a file with a large header.
+# This is line 3177 of a file with a large header.
+# This is line 3178 of a file with a large header.
+# This is line 3179 of a file with a large header.
+# This is line 3180 of a file with a large header.
+# This is line 3181 of a file with a large header.
+# This is line 3182 of a file with a large header.
+# This is line 3183 of a file with a large header.
+# This is line 3184 of a file with a large header.
+# This is line 3185 of a file with a large header.
+# This is line 3186 of a file with a large header.
+# This is line 3187 of a file with a large header.
+# This is line 3188 of a file with a large header.
+# This is line 3189 of a file with a large header.
+# This is line 3190 of a file with a large header.
+# This is line 3191 of a file with a large header.
+# This is line 3192 of a file with a large header.
+# This is line 3193 of a file with a large header.
+# This is line 3194 of a file with a large header.
+# This is line 3195 of a file with a large header.
+# This is line 3196 of a file with a large header.
+# This is line 3197 of a file with a large header.
+# This is line 3198 of a file with a large header.
+# This is line 3199 of a file with a large header.
+# This is line 3200 of a file with a large header.
+# This is line 3201 of a file with a large header.
+# This is line 3202 of a file with a large header.
+# This is line 3203 of a file with a large header.
+# This is line 3204 of a file with a large header.
+# This is line 3205 of a file with a large header.
+# This is line 3206 of a file with a large header.
+# This is line 3207 of a file with a large header.
+# This is line 3208 of a file with a large header.
+# This is line 3209 of a file with a large header.
+# This is line 3210 of a file with a large header.
+# This is line 3211 of a file with a large header.
+# This is line 3212 of a file with a large header.
+# This is line 3213 of a file with a large header.
+# This is line 3214 of a file with a large header.
+# This is line 3215 of a file with a large header.
+# This is line 3216 of a file with a large header.
+# This is line 3217 of a file with a large header.
+# This is line 3218 of a file with a large header.
+# This is line 3219 of a file with a large header.
+# This is line 3220 of a file with a large header.
+# This is line 3221 of a file with a large header.
+# This is line 3222 of a file with a large header.
+# This is line 3223 of a file with a large header.
+# This is line 3224 of a file with a large header.
+# This is line 3225 of a file with a large header.
+# This is line 3226 of a file with a large header.
+# This is line 3227 of a file with a large header.
+# This is line 3228 of a file with a large header.
+# This is line 3229 of a file with a large header.
+# This is line 3230 of a file with a large header.
+# This is line 3231 of a file with a large header.
+# This is line 3232 of a file with a large header.
+# This is line 3233 of a file with a large header.
+# This is line 3234 of a file with a large header.
+# This is line 3235 of a file with a large header.
+# This is line 3236 of a file with a large header.
+# This is line 3237 of a file with a large header.
+# This is line 3238 of a file with a large header.
+# This is line 3239 of a file with a large header.
+# This is line 3240 of a file with a large header.
+# This is line 3241 of a file with a large header.
+# This is line 3242 of a file with a large header.
+# This is line 3243 of a file with a large header.
+# This is line 3244 of a file with a large header.
+# This is line 3245 of a file with a large header.
+# This is line 3246 of a file with a large header.
+# This is line 3247 of a file with a large header.
+# This is line 3248 of a file with a large header.
+# This is line 3249 of a file with a large header.
+# This is line 3250 of a file with a large header.
+# This is line 3251 of a file with a large header.
+# This is line 3252 of a file with a large header.
+# This is line 3253 of a file with a large header.
+# This is line 3254 of a file with a large header.
+# This is line 3255 of a file with a large header.
+# This is line 3256 of a file with a large header.
+# This is line 3257 of a file with a large header.
+# This is line 3258 of a file with a large header.
+# This is line 3259 of a file with a large header.
+# This is line 3260 of a file with a large header.
+# This is line 3261 of a file with a large header.
+# This is line 3262 of a file with a large header.
+# This is line 3263 of a file with a large header.
+# This is line 3264 of a file with a large header.
+# This is line 3265 of a file with a large header.
+# This is line 3266 of a file with a large header.
+# This is line 3267 of a file with a large header.
+# This is line 3268 of a file with a large header.
+# This is line 3269 of a file with a large header.
+# This is line 3270 of a file with a large header.
+# This is line 3271 of a file with a large header.
+# This is line 3272 of a file with a large header.
+# This is line 3273 of a file with a large header.
+# This is line 3274 of a file with a large header.
+# This is line 3275 of a file with a large header.
+# This is line 3276 of a file with a large header.
+# This is line 3277 of a file with a large header.
+# This is line 3278 of a file with a large header.
+# This is line 3279 of a file with a large header.
+# This is line 3280 of a file with a large header.
+# This is line 3281 of a file with a large header.
+# This is line 3282 of a file with a large header.
+# This is line 3283 of a file with a large header.
+# This is line 3284 of a file with a large header.
+# This is line 3285 of a file with a large header.
+# This is line 3286 of a file with a large header.
+# This is line 3287 of a file with a large header.
+# This is line 3288 of a file with a large header.
+# This is line 3289 of a file with a large header.
+# This is line 3290 of a file with a large header.
+# This is line 3291 of a file with a large header.
+# This is line 3292 of a file with a large header.
+# This is line 3293 of a file with a large header.
+# This is line 3294 of a file with a large header.
+# This is line 3295 of a file with a large header.
+# This is line 3296 of a file with a large header.
+# This is line 3297 of a file with a large header.
+# This is line 3298 of a file with a large header.
+# This is line 3299 of a file with a large header.
+# This is line 3300 of a file with a large header.
+# This is line 3301 of a file with a large header.
+# This is line 3302 of a file with a large header.
+# This is line 3303 of a file with a large header.
+# This is line 3304 of a file with a large header.
+# This is line 3305 of a file with a large header.
+# This is line 3306 of a file with a large header.
+# This is line 3307 of a file with a large header.
+# This is line 3308 of a file with a large header.
+# This is line 3309 of a file with a large header.
+# This is line 3310 of a file with a large header.
+# This is line 3311 of a file with a large header.
+# This is line 3312 of a file with a large header.
+# This is line 3313 of a file with a large header.
+# This is line 3314 of a file with a large header.
+# This is line 3315 of a file with a large header.
+# This is line 3316 of a file with a large header.
+# This is line 3317 of a file with a large header.
+# This is line 3318 of a file with a large header.
+# This is line 3319 of a file with a large header.
+# This is line 3320 of a file with a large header.
+# This is line 3321 of a file with a large header.
+# This is line 3322 of a file with a large header.
+# This is line 3323 of a file with a large header.
+# This is line 3324 of a file with a large header.
+# This is line 3325 of a file with a large header.
+# This is line 3326 of a file with a large header.
+# This is line 3327 of a file with a large header.
+# This is line 3328 of a file with a large header.
+# This is line 3329 of a file with a large header.
+# This is line 3330 of a file with a large header.
+# This is line 3331 of a file with a large header.
+# This is line 3332 of a file with a large header.
+# This is line 3333 of a file with a large header.
+# This is line 3334 of a file with a large header.
+# This is line 3335 of a file with a large header.
+# This is line 3336 of a file with a large header.
+# This is line 3337 of a file with a large header.
+# This is line 3338 of a file with a large header.
+# This is line 3339 of a file with a large header.
+# This is line 3340 of a file with a large header.
+# This is line 3341 of a file with a large header.
+# This is line 3342 of a file with a large header.
+# This is line 3343 of a file with a large header.
+# This is line 3344 of a file with a large header.
+# This is line 3345 of a file with a large header.
+# This is line 3346 of a file with a large header.
+# This is line 3347 of a file with a large header.
+# This is line 3348 of a file with a large header.
+# This is line 3349 of a file with a large header.
+# This is line 3350 of a file with a large header.
+# This is line 3351 of a file with a large header.
+# This is line 3352 of a file with a large header.
+# This is line 3353 of a file with a large header.
+# This is line 3354 of a file with a large header.
+# This is line 3355 of a file with a large header.
+# This is line 3356 of a file with a large header.
+# This is line 3357 of a file with a large header.
+# This is line 3358 of a file with a large header.
+# This is line 3359 of a file with a large header.
+# This is line 3360 of a file with a large header.
+# This is line 3361 of a file with a large header.
+# This is line 3362 of a file with a large header.
+# This is line 3363 of a file with a large header.
+# This is line 3364 of a file with a large header.
+# This is line 3365 of a file with a large header.
+# This is line 3366 of a file with a large header.
+# This is line 3367 of a file with a large header.
+# This is line 3368 of a file with a large header.
+# This is line 3369 of a file with a large header.
+# This is line 3370 of a file with a large header.
+# This is line 3371 of a file with a large header.
+# This is line 3372 of a file with a large header.
+# This is line 3373 of a file with a large header.
+# This is line 3374 of a file with a large header.
+# This is line 3375 of a file with a large header.
+# This is line 3376 of a file with a large header.
+# This is line 3377 of a file with a large header.
+# This is line 3378 of a file with a large header.
+# This is line 3379 of a file with a large header.
+# This is line 3380 of a file with a large header.
+# This is line 3381 of a file with a large header.
+# This is line 3382 of a file with a large header.
+# This is line 3383 of a file with a large header.
+# This is line 3384 of a file with a large header.
+# This is line 3385 of a file with a large header.
+# This is line 3386 of a file with a large header.
+# This is line 3387 of a file with a large header.
+# This is line 3388 of a file with a large header.
+# This is line 3389 of a file with a large header.
+# This is line 3390 of a file with a large header.
+# This is line 3391 of a file with a large header.
+# This is line 3392 of a file with a large header.
+# This is line 3393 of a file with a large header.
+# This is line 3394 of a file with a large header.
+# This is line 3395 of a file with a large header.
+# This is line 3396 of a file with a large header.
+# This is line 3397 of a file with a large header.
+# This is line 3398 of a file with a large header.
+# This is line 3399 of a file with a large header.
+# This is line 3400 of a file with a large header.
+# This is line 3401 of a file with a large header.
+# This is line 3402 of a file with a large header.
+# This is line 3403 of a file with a large header.
+# This is line 3404 of a file with a large header.
+# This is line 3405 of a file with a large header.
+# This is line 3406 of a file with a large header.
+# This is line 3407 of a file with a large header.
+# This is line 3408 of a file with a large header.
+# This is line 3409 of a file with a large header.
+# This is line 3410 of a file with a large header.
+# This is line 3411 of a file with a large header.
+# This is line 3412 of a file with a large header.
+# This is line 3413 of a file with a large header.
+# This is line 3414 of a file with a large header.
+# This is line 3415 of a file with a large header.
+# This is line 3416 of a file with a large header.
+# This is line 3417 of a file with a large header.
+# This is line 3418 of a file with a large header.
+# This is line 3419 of a file with a large header.
+# This is line 3420 of a file with a large header.
+# This is line 3421 of a file with a large header.
+# This is line 3422 of a file with a large header.
+# This is line 3423 of a file with a large header.
+# This is line 3424 of a file with a large header.
+# This is line 3425 of a file with a large header.
+# This is line 3426 of a file with a large header.
+# This is line 3427 of a file with a large header.
+# This is line 3428 of a file with a large header.
+# This is line 3429 of a file with a large header.
+# This is line 3430 of a file with a large header.
+# This is line 3431 of a file with a large header.
+# This is line 3432 of a file with a large header.
+# This is line 3433 of a file with a large header.
+# This is line 3434 of a file with a large header.
+# This is line 3435 of a file with a large header.
+# This is line 3436 of a file with a large header.
+# This is line 3437 of a file with a large header.
+# This is line 3438 of a file with a large header.
+# This is line 3439 of a file with a large header.
+# This is line 3440 of a file with a large header.
+# This is line 3441 of a file with a large header.
+# This is line 3442 of a file with a large header.
+# This is line 3443 of a file with a large header.
+# This is line 3444 of a file with a large header.
+# This is line 3445 of a file with a large header.
+# This is line 3446 of a file with a large header.
+# This is line 3447 of a file with a large header.
+# This is line 3448 of a file with a large header.
+# This is line 3449 of a file with a large header.
+# This is line 3450 of a file with a large header.
+# This is line 3451 of a file with a large header.
+# This is line 3452 of a file with a large header.
+# This is line 3453 of a file with a large header.
+# This is line 3454 of a file with a large header.
+# This is line 3455 of a file with a large header.
+# This is line 3456 of a file with a large header.
+# This is line 3457 of a file with a large header.
+# This is line 3458 of a file with a large header.
+# This is line 3459 of a file with a large header.
+# This is line 3460 of a file with a large header.
+# This is line 3461 of a file with a large header.
+# This is line 3462 of a file with a large header.
+# This is line 3463 of a file with a large header.
+# This is line 3464 of a file with a large header.
+# This is line 3465 of a file with a large header.
+# This is line 3466 of a file with a large header.
+# This is line 3467 of a file with a large header.
+# This is line 3468 of a file with a large header.
+# This is line 3469 of a file with a large header.
+# This is line 3470 of a file with a large header.
+# This is line 3471 of a file with a large header.
+# This is line 3472 of a file with a large header.
+# This is line 3473 of a file with a large header.
+# This is line 3474 of a file with a large header.
+# This is line 3475 of a file with a large header.
+# This is line 3476 of a file with a large header.
+# This is line 3477 of a file with a large header.
+# This is line 3478 of a file with a large header.
+# This is line 3479 of a file with a large header.
+# This is line 3480 of a file with a large header.
+# This is line 3481 of a file with a large header.
+# This is line 3482 of a file with a large header.
+# This is line 3483 of a file with a large header.
+# This is line 3484 of a file with a large header.
+# This is line 3485 of a file with a large header.
+# This is line 3486 of a file with a large header.
+# This is line 3487 of a file with a large header.
+# This is line 3488 of a file with a large header.
+# This is line 3489 of a file with a large header.
+# This is line 3490 of a file with a large header.
+# This is line 3491 of a file with a large header.
+# This is line 3492 of a file with a large header.
+# This is line 3493 of a file with a large header.
+# This is line 3494 of a file with a large header.
+# This is line 3495 of a file with a large header.
+# This is line 3496 of a file with a large header.
+# This is line 3497 of a file with a large header.
+# This is line 3498 of a file with a large header.
+# This is line 3499 of a file with a large header.
+# This is line 3500 of a file with a large header.
+# This is line 3501 of a file with a large header.
+# This is line 3502 of a file with a large header.
+# This is line 3503 of a file with a large header.
+# This is line 3504 of a file with a large header.
+# This is line 3505 of a file with a large header.
+# This is line 3506 of a file with a large header.
+# This is line 3507 of a file with a large header.
+# This is line 3508 of a file with a large header.
+# This is line 3509 of a file with a large header.
+# This is line 3510 of a file with a large header.
+# This is line 3511 of a file with a large header.
+# This is line 3512 of a file with a large header.
+# This is line 3513 of a file with a large header.
+# This is line 3514 of a file with a large header.
+# This is line 3515 of a file with a large header.
+# This is line 3516 of a file with a large header.
+# This is line 3517 of a file with a large header.
+# This is line 3518 of a file with a large header.
+# This is line 3519 of a file with a large header.
+# This is line 3520 of a file with a large header.
+# This is line 3521 of a file with a large header.
+# This is line 3522 of a file with a large header.
+# This is line 3523 of a file with a large header.
+# This is line 3524 of a file with a large header.
+# This is line 3525 of a file with a large header.
+# This is line 3526 of a file with a large header.
+# This is line 3527 of a file with a large header.
+# This is line 3528 of a file with a large header.
+# This is line 3529 of a file with a large header.
+# This is line 3530 of a file with a large header.
+# This is line 3531 of a file with a large header.
+# This is line 3532 of a file with a large header.
+# This is line 3533 of a file with a large header.
+# This is line 3534 of a file with a large header.
+# This is line 3535 of a file with a large header.
+# This is line 3536 of a file with a large header.
+# This is line 3537 of a file with a large header.
+# This is line 3538 of a file with a large header.
+# This is line 3539 of a file with a large header.
+# This is line 3540 of a file with a large header.
+# This is line 3541 of a file with a large header.
+# This is line 3542 of a file with a large header.
+# This is line 3543 of a file with a large header.
+# This is line 3544 of a file with a large header.
+# This is line 3545 of a file with a large header.
+# This is line 3546 of a file with a large header.
+# This is line 3547 of a file with a large header.
+# This is line 3548 of a file with a large header.
+# This is line 3549 of a file with a large header.
+# This is line 3550 of a file with a large header.
+# This is line 3551 of a file with a large header.
+# This is line 3552 of a file with a large header.
+# This is line 3553 of a file with a large header.
+# This is line 3554 of a file with a large header.
+# This is line 3555 of a file with a large header.
+# This is line 3556 of a file with a large header.
+# This is line 3557 of a file with a large header.
+# This is line 3558 of a file with a large header.
+# This is line 3559 of a file with a large header.
+# This is line 3560 of a file with a large header.
+# This is line 3561 of a file with a large header.
+# This is line 3562 of a file with a large header.
+# This is line 3563 of a file with a large header.
+# This is line 3564 of a file with a large header.
+# This is line 3565 of a file with a large header.
+# This is line 3566 of a file with a large header.
+# This is line 3567 of a file with a large header.
+# This is line 3568 of a file with a large header.
+# This is line 3569 of a file with a large header.
+# This is line 3570 of a file with a large header.
+# This is line 3571 of a file with a large header.
+# This is line 3572 of a file with a large header.
+# This is line 3573 of a file with a large header.
+# This is line 3574 of a file with a large header.
+# This is line 3575 of a file with a large header.
+# This is line 3576 of a file with a large header.
+# This is line 3577 of a file with a large header.
+# This is line 3578 of a file with a large header.
+# This is line 3579 of a file with a large header.
+# This is line 3580 of a file with a large header.
+# This is line 3581 of a file with a large header.
+# This is line 3582 of a file with a large header.
+# This is line 3583 of a file with a large header.
+# This is line 3584 of a file with a large header.
+# This is line 3585 of a file with a large header.
+# This is line 3586 of a file with a large header.
+# This is line 3587 of a file with a large header.
+# This is line 3588 of a file with a large header.
+# This is line 3589 of a file with a large header.
+# This is line 3590 of a file with a large header.
+# This is line 3591 of a file with a large header.
+# This is line 3592 of a file with a large header.
+# This is line 3593 of a file with a large header.
+# This is line 3594 of a file with a large header.
+# This is line 3595 of a file with a large header.
+# This is line 3596 of a file with a large header.
+# This is line 3597 of a file with a large header.
+# This is line 3598 of a file with a large header.
+# This is line 3599 of a file with a large header.
+# This is line 3600 of a file with a large header.
+# This is line 3601 of a file with a large header.
+# This is line 3602 of a file with a large header.
+# This is line 3603 of a file with a large header.
+# This is line 3604 of a file with a large header.
+# This is line 3605 of a file with a large header.
+# This is line 3606 of a file with a large header.
+# This is line 3607 of a file with a large header.
+# This is line 3608 of a file with a large header.
+# This is line 3609 of a file with a large header.
+# This is line 3610 of a file with a large header.
+# This is line 3611 of a file with a large header.
+# This is line 3612 of a file with a large header.
+# This is line 3613 of a file with a large header.
+# This is line 3614 of a file with a large header.
+# This is line 3615 of a file with a large header.
+# This is line 3616 of a file with a large header.
+# This is line 3617 of a file with a large header.
+# This is line 3618 of a file with a large header.
+# This is line 3619 of a file with a large header.
+# This is line 3620 of a file with a large header.
+# This is line 3621 of a file with a large header.
+# This is line 3622 of a file with a large header.
+# This is line 3623 of a file with a large header.
+# This is line 3624 of a file with a large header.
+# This is line 3625 of a file with a large header.
+# This is line 3626 of a file with a large header.
+# This is line 3627 of a file with a large header.
+# This is line 3628 of a file with a large header.
+# This is line 3629 of a file with a large header.
+# This is line 3630 of a file with a large header.
+# This is line 3631 of a file with a large header.
+# This is line 3632 of a file with a large header.
+# This is line 3633 of a file with a large header.
+# This is line 3634 of a file with a large header.
+# This is line 3635 of a file with a large header.
+# This is line 3636 of a file with a large header.
+# This is line 3637 of a file with a large header.
+# This is line 3638 of a file with a large header.
+# This is line 3639 of a file with a large header.
+# This is line 3640 of a file with a large header.
+# This is line 3641 of a file with a large header.
+# This is line 3642 of a file with a large header.
+# This is line 3643 of a file with a large header.
+# This is line 3644 of a file with a large header.
+# This is line 3645 of a file with a large header.
+# This is line 3646 of a file with a large header.
+# This is line 3647 of a file with a large header.
+# This is line 3648 of a file with a large header.
+# This is line 3649 of a file with a large header.
+# This is line 3650 of a file with a large header.
+# This is line 3651 of a file with a large header.
+# This is line 3652 of a file with a large header.
+# This is line 3653 of a file with a large header.
+# This is line 3654 of a file with a large header.
+# This is line 3655 of a file with a large header.
+# This is line 3656 of a file with a large header.
+# This is line 3657 of a file with a large header.
+# This is line 3658 of a file with a large header.
+# This is line 3659 of a file with a large header.
+# This is line 3660 of a file with a large header.
+# This is line 3661 of a file with a large header.
+# This is line 3662 of a file with a large header.
+# This is line 3663 of a file with a large header.
+# This is line 3664 of a file with a large header.
+# This is line 3665 of a file with a large header.
+# This is line 3666 of a file with a large header.
+# This is line 3667 of a file with a large header.
+# This is line 3668 of a file with a large header.
+# This is line 3669 of a file with a large header.
+# This is line 3670 of a file with a large header.
+# This is line 3671 of a file with a large header.
+# This is line 3672 of a file with a large header.
+# This is line 3673 of a file with a large header.
+# This is line 3674 of a file with a large header.
+# This is line 3675 of a file with a large header.
+# This is line 3676 of a file with a large header.
+# This is line 3677 of a file with a large header.
+# This is line 3678 of a file with a large header.
+# This is line 3679 of a file with a large header.
+# This is line 3680 of a file with a large header.
+# This is line 3681 of a file with a large header.
+# This is line 3682 of a file with a large header.
+# This is line 3683 of a file with a large header.
+# This is line 3684 of a file with a large header.
+# This is line 3685 of a file with a large header.
+# This is line 3686 of a file with a large header.
+# This is line 3687 of a file with a large header.
+# This is line 3688 of a file with a large header.
+# This is line 3689 of a file with a large header.
+# This is line 3690 of a file with a large header.
+# This is line 3691 of a file with a large header.
+# This is line 3692 of a file with a large header.
+# This is line 3693 of a file with a large header.
+# This is line 3694 of a file with a large header.
+# This is line 3695 of a file with a large header.
+# This is line 3696 of a file with a large header.
+# This is line 3697 of a file with a large header.
+# This is line 3698 of a file with a large header.
+# This is line 3699 of a file with a large header.
+# This is line 3700 of a file with a large header.
+# This is line 3701 of a file with a large header.
+# This is line 3702 of a file with a large header.
+# This is line 3703 of a file with a large header.
+# This is line 3704 of a file with a large header.
+# This is line 3705 of a file with a large header.
+# This is line 3706 of a file with a large header.
+# This is line 3707 of a file with a large header.
+# This is line 3708 of a file with a large header.
+# This is line 3709 of a file with a large header.
+# This is line 3710 of a file with a large header.
+# This is line 3711 of a file with a large header.
+# This is line 3712 of a file with a large header.
+# This is line 3713 of a file with a large header.
+# This is line 3714 of a file with a large header.
+# This is line 3715 of a file with a large header.
+# This is line 3716 of a file with a large header.
+# This is line 3717 of a file with a large header.
+# This is line 3718 of a file with a large header.
+# This is line 3719 of a file with a large header.
+# This is line 3720 of a file with a large header.
+# This is line 3721 of a file with a large header.
+# This is line 3722 of a file with a large header.
+# This is line 3723 of a file with a large header.
+# This is line 3724 of a file with a large header.
+# This is line 3725 of a file with a large header.
+# This is line 3726 of a file with a large header.
+# This is line 3727 of a file with a large header.
+# This is line 3728 of a file with a large header.
+# This is line 3729 of a file with a large header.
+# This is line 3730 of a file with a large header.
+# This is line 3731 of a file with a large header.
+# This is line 3732 of a file with a large header.
+# This is line 3733 of a file with a large header.
+# This is line 3734 of a file with a large header.
+# This is line 3735 of a file with a large header.
+# This is line 3736 of a file with a large header.
+# This is line 3737 of a file with a large header.
+# This is line 3738 of a file with a large header.
+# This is line 3739 of a file with a large header.
+# This is line 3740 of a file with a large header.
+# This is line 3741 of a file with a large header.
+# This is line 3742 of a file with a large header.
+# This is line 3743 of a file with a large header.
+# This is line 3744 of a file with a large header.
+# This is line 3745 of a file with a large header.
+# This is line 3746 of a file with a large header.
+# This is line 3747 of a file with a large header.
+# This is line 3748 of a file with a large header.
+# This is line 3749 of a file with a large header.
+# This is line 3750 of a file with a large header.
+# This is line 3751 of a file with a large header.
+# This is line 3752 of a file with a large header.
+# This is line 3753 of a file with a large header.
+# This is line 3754 of a file with a large header.
+# This is line 3755 of a file with a large header.
+# This is line 3756 of a file with a large header.
+# This is line 3757 of a file with a large header.
+# This is line 3758 of a file with a large header.
+# This is line 3759 of a file with a large header.
+# This is line 3760 of a file with a large header.
+# This is line 3761 of a file with a large header.
+# This is line 3762 of a file with a large header.
+# This is line 3763 of a file with a large header.
+# This is line 3764 of a file with a large header.
+# This is line 3765 of a file with a large header.
+# This is line 3766 of a file with a large header.
+# This is line 3767 of a file with a large header.
+# This is line 3768 of a file with a large header.
+# This is line 3769 of a file with a large header.
+# This is line 3770 of a file with a large header.
+# This is line 3771 of a file with a large header.
+# This is line 3772 of a file with a large header.
+# This is line 3773 of a file with a large header.
+# This is line 3774 of a file with a large header.
+# This is line 3775 of a file with a large header.
+# This is line 3776 of a file with a large header.
+# This is line 3777 of a file with a large header.
+# This is line 3778 of a file with a large header.
+# This is line 3779 of a file with a large header.
+# This is line 3780 of a file with a large header.
+# This is line 3781 of a file with a large header.
+# This is line 3782 of a file with a large header.
+# This is line 3783 of a file with a large header.
+# This is line 3784 of a file with a large header.
+# This is line 3785 of a file with a large header.
+# This is line 3786 of a file with a large header.
+# This is line 3787 of a file with a large header.
+# This is line 3788 of a file with a large header.
+# This is line 3789 of a file with a large header.
+# This is line 3790 of a file with a large header.
+# This is line 3791 of a file with a large header.
+# This is line 3792 of a file with a large header.
+# This is line 3793 of a file with a large header.
+# This is line 3794 of a file with a large header.
+# This is line 3795 of a file with a large header.
+# This is line 3796 of a file with a large header.
+# This is line 3797 of a file with a large header.
+# This is line 3798 of a file with a large header.
+# This is line 3799 of a file with a large header.
+# This is line 3800 of a file with a large header.
+# This is line 3801 of a file with a large header.
+# This is line 3802 of a file with a large header.
+# This is line 3803 of a file with a large header.
+# This is line 3804 of a file with a large header.
+# This is line 3805 of a file with a large header.
+# This is line 3806 of a file with a large header.
+# This is line 3807 of a file with a large header.
+# This is line 3808 of a file with a large header.
+# This is line 3809 of a file with a large header.
+# This is line 3810 of a file with a large header.
+# This is line 3811 of a file with a large header.
+# This is line 3812 of a file with a large header.
+# This is line 3813 of a file with a large header.
+# This is line 3814 of a file with a large header.
+# This is line 3815 of a file with a large header.
+# This is line 3816 of a file with a large header.
+# This is line 3817 of a file with a large header.
+# This is line 3818 of a file with a large header.
+# This is line 3819 of a file with a large header.
+# This is line 3820 of a file with a large header.
+# This is line 3821 of a file with a large header.
+# This is line 3822 of a file with a large header.
+# This is line 3823 of a file with a large header.
+# This is line 3824 of a file with a large header.
+# This is line 3825 of a file with a large header.
+# This is line 3826 of a file with a large header.
+# This is line 3827 of a file with a large header.
+# This is line 3828 of a file with a large header.
+# This is line 3829 of a file with a large header.
+# This is line 3830 of a file with a large header.
+# This is line 3831 of a file with a large header.
+# This is line 3832 of a file with a large header.
+# This is line 3833 of a file with a large header.
+# This is line 3834 of a file with a large header.
+# This is line 3835 of a file with a large header.
+# This is line 3836 of a file with a large header.
+# This is line 3837 of a file with a large header.
+# This is line 3838 of a file with a large header.
+# This is line 3839 of a file with a large header.
+# This is line 3840 of a file with a large header.
+# This is line 3841 of a file with a large header.
+# This is line 3842 of a file with a large header.
+# This is line 3843 of a file with a large header.
+# This is line 3844 of a file with a large header.
+# This is line 3845 of a file with a large header.
+# This is line 3846 of a file with a large header.
+# This is line 3847 of a file with a large header.
+# This is line 3848 of a file with a large header.
+# This is line 3849 of a file with a large header.
+# This is line 3850 of a file with a large header.
+# This is line 3851 of a file with a large header.
+# This is line 3852 of a file with a large header.
+# This is line 3853 of a file with a large header.
+# This is line 3854 of a file with a large header.
+# This is line 3855 of a file with a large header.
+# This is line 3856 of a file with a large header.
+# This is line 3857 of a file with a large header.
+# This is line 3858 of a file with a large header.
+# This is line 3859 of a file with a large header.
+# This is line 3860 of a file with a large header.
+# This is line 3861 of a file with a large header.
+# This is line 3862 of a file with a large header.
+# This is line 3863 of a file with a large header.
+# This is line 3864 of a file with a large header.
+# This is line 3865 of a file with a large header.
+# This is line 3866 of a file with a large header.
+# This is line 3867 of a file with a large header.
+# This is line 3868 of a file with a large header.
+# This is line 3869 of a file with a large header.
+# This is line 3870 of a file with a large header.
+# This is line 3871 of a file with a large header.
+# This is line 3872 of a file with a large header.
+# This is line 3873 of a file with a large header.
+# This is line 3874 of a file with a large header.
+# This is line 3875 of a file with a large header.
+# This is line 3876 of a file with a large header.
+# This is line 3877 of a file with a large header.
+# This is line 3878 of a file with a large header.
+# This is line 3879 of a file with a large header.
+# This is line 3880 of a file with a large header.
+# This is line 3881 of a file with a large header.
+# This is line 3882 of a file with a large header.
+# This is line 3883 of a file with a large header.
+# This is line 3884 of a file with a large header.
+# This is line 3885 of a file with a large header.
+# This is line 3886 of a file with a large header.
+# This is line 3887 of a file with a large header.
+# This is line 3888 of a file with a large header.
+# This is line 3889 of a file with a large header.
+# This is line 3890 of a file with a large header.
+# This is line 3891 of a file with a large header.
+# This is line 3892 of a file with a large header.
+# This is line 3893 of a file with a large header.
+# This is line 3894 of a file with a large header.
+# This is line 3895 of a file with a large header.
+# This is line 3896 of a file with a large header.
+# This is line 3897 of a file with a large header.
+# This is line 3898 of a file with a large header.
+# This is line 3899 of a file with a large header.
+# This is line 3900 of a file with a large header.
+# This is line 3901 of a file with a large header.
+# This is line 3902 of a file with a large header.
+# This is line 3903 of a file with a large header.
+# This is line 3904 of a file with a large header.
+# This is line 3905 of a file with a large header.
+# This is line 3906 of a file with a large header.
+# This is line 3907 of a file with a large header.
+# This is line 3908 of a file with a large header.
+# This is line 3909 of a file with a large header.
+# This is line 3910 of a file with a large header.
+# This is line 3911 of a file with a large header.
+# This is line 3912 of a file with a large header.
+# This is line 3913 of a file with a large header.
+# This is line 3914 of a file with a large header.
+# This is line 3915 of a file with a large header.
+# This is line 3916 of a file with a large header.
+# This is line 3917 of a file with a large header.
+# This is line 3918 of a file with a large header.
+# This is line 3919 of a file with a large header.
+# This is line 3920 of a file with a large header.
+# This is line 3921 of a file with a large header.
+# This is line 3922 of a file with a large header.
+# This is line 3923 of a file with a large header.
+# This is line 3924 of a file with a large header.
+# This is line 3925 of a file with a large header.
+# This is line 3926 of a file with a large header.
+# This is line 3927 of a file with a large header.
+# This is line 3928 of a file with a large header.
+# This is line 3929 of a file with a large header.
+# This is line 3930 of a file with a large header.
+# This is line 3931 of a file with a large header.
+# This is line 3932 of a file with a large header.
+# This is line 3933 of a file with a large header.
+# This is line 3934 of a file with a large header.
+# This is line 3935 of a file with a large header.
+# This is line 3936 of a file with a large header.
+# This is line 3937 of a file with a large header.
+# This is line 3938 of a file with a large header.
+# This is line 3939 of a file with a large header.
+# This is line 3940 of a file with a large header.
+# This is line 3941 of a file with a large header.
+# This is line 3942 of a file with a large header.
+# This is line 3943 of a file with a large header.
+# This is line 3944 of a file with a large header.
+# This is line 3945 of a file with a large header.
+# This is line 3946 of a file with a large header.
+# This is line 3947 of a file with a large header.
+# This is line 3948 of a file with a large header.
+# This is line 3949 of a file with a large header.
+# This is line 3950 of a file with a large header.
+# This is line 3951 of a file with a large header.
+# This is line 3952 of a file with a large header.
+# This is line 3953 of a file with a large header.
+# This is line 3954 of a file with a large header.
+# This is line 3955 of a file with a large header.
+# This is line 3956 of a file with a large header.
+# This is line 3957 of a file with a large header.
+# This is line 3958 of a file with a large header.
+# This is line 3959 of a file with a large header.
+# This is line 3960 of a file with a large header.
+# This is line 3961 of a file with a large header.
+# This is line 3962 of a file with a large header.
+# This is line 3963 of a file with a large header.
+# This is line 3964 of a file with a large header.
+# This is line 3965 of a file with a large header.
+# This is line 3966 of a file with a large header.
+# This is line 3967 of a file with a large header.
+# This is line 3968 of a file with a large header.
+# This is line 3969 of a file with a large header.
+# This is line 3970 of a file with a large header.
+# This is line 3971 of a file with a large header.
+# This is line 3972 of a file with a large header.
+# This is line 3973 of a file with a large header.
+# This is line 3974 of a file with a large header.
+# This is line 3975 of a file with a large header.
+# This is line 3976 of a file with a large header.
+# This is line 3977 of a file with a large header.
+# This is line 3978 of a file with a large header.
+# This is line 3979 of a file with a large header.
+# This is line 3980 of a file with a large header.
+# This is line 3981 of a file with a large header.
+# This is line 3982 of a file with a large header.
+# This is line 3983 of a file with a large header.
+# This is line 3984 of a file with a large header.
+# This is line 3985 of a file with a large header.
+# This is line 3986 of a file with a large header.
+# This is line 3987 of a file with a large header.
+# This is line 3988 of a file with a large header.
+# This is line 3989 of a file with a large header.
+# This is line 3990 of a file with a large header.
+# This is line 3991 of a file with a large header.
+# This is line 3992 of a file with a large header.
+# This is line 3993 of a file with a large header.
+# This is line 3994 of a file with a large header.
+# This is line 3995 of a file with a large header.
+# This is line 3996 of a file with a large header.
+# This is line 3997 of a file with a large header.
+# This is line 3998 of a file with a large header.
+# This is line 3999 of a file with a large header.
+chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -
diff --git a/test/intersect/a_bgzipped.bed.gz b/test/intersect/a_bgzipped.bed.gz
new file mode 100644
index 0000000..b483225
Binary files /dev/null and b/test/intersect/a_bgzipped.bed.gz differ
diff --git a/test/intersect/a_gzipped.bed.gz b/test/intersect/a_gzipped.bed.gz
new file mode 100644
index 0000000..745284b
Binary files /dev/null and b/test/intersect/a_gzipped.bed.gz differ
diff --git a/test/intersect/a_withLargeHeader.bed b/test/intersect/a_withLargeHeader.bed
new file mode 100644
index 0000000..612abe0
--- /dev/null
+++ b/test/intersect/a_withLargeHeader.bed
@@ -0,0 +1,4002 @@
+# This is line 0 of a file with a large header.
+# This is line 1 of a file with a large header.
+# This is line 2 of a file with a large header.
+# This is line 3 of a file with a large header.
+# This is line 4 of a file with a large header.
+# This is line 5 of a file with a large header.
+# This is line 6 of a file with a large header.
+# This is line 7 of a file with a large header.
+# This is line 8 of a file with a large header.
+# This is line 9 of a file with a large header.
+# This is line 10 of a file with a large header.
+# This is line 11 of a file with a large header.
+# This is line 12 of a file with a large header.
+# This is line 13 of a file with a large header.
+# This is line 14 of a file with a large header.
+# This is line 15 of a file with a large header.
+# This is line 16 of a file with a large header.
+# This is line 17 of a file with a large header.
+# This is line 18 of a file with a large header.
+# This is line 19 of a file with a large header.
+# This is line 20 of a file with a large header.
+# This is line 21 of a file with a large header.
+# This is line 22 of a file with a large header.
+# This is line 23 of a file with a large header.
+# This is line 24 of a file with a large header.
+# This is line 25 of a file with a large header.
+# This is line 26 of a file with a large header.
+# This is line 27 of a file with a large header.
+# This is line 28 of a file with a large header.
+# This is line 29 of a file with a large header.
+# This is line 30 of a file with a large header.
+# This is line 31 of a file with a large header.
+# This is line 32 of a file with a large header.
+# This is line 33 of a file with a large header.
+# This is line 34 of a file with a large header.
+# This is line 35 of a file with a large header.
+# This is line 36 of a file with a large header.
+# This is line 37 of a file with a large header.
+# This is line 38 of a file with a large header.
+# This is line 39 of a file with a large header.
+# This is line 40 of a file with a large header.
+# This is line 41 of a file with a large header.
+# This is line 42 of a file with a large header.
+# This is line 43 of a file with a large header.
+# This is line 44 of a file with a large header.
+# This is line 45 of a file with a large header.
+# This is line 46 of a file with a large header.
+# This is line 47 of a file with a large header.
+# This is line 48 of a file with a large header.
+# This is line 49 of a file with a large header.
+# This is line 50 of a file with a large header.
+# This is line 51 of a file with a large header.
+# This is line 52 of a file with a large header.
+# This is line 53 of a file with a large header.
+# This is line 54 of a file with a large header.
+# This is line 55 of a file with a large header.
+# This is line 56 of a file with a large header.
+# This is line 57 of a file with a large header.
+# This is line 58 of a file with a large header.
+# This is line 59 of a file with a large header.
+# This is line 60 of a file with a large header.
+# This is line 61 of a file with a large header.
+# This is line 62 of a file with a large header.
+# This is line 63 of a file with a large header.
+# This is line 64 of a file with a large header.
+# This is line 65 of a file with a large header.
+# This is line 66 of a file with a large header.
+# This is line 67 of a file with a large header.
+# This is line 68 of a file with a large header.
+# This is line 69 of a file with a large header.
+# This is line 70 of a file with a large header.
+# This is line 71 of a file with a large header.
+# This is line 72 of a file with a large header.
+# This is line 73 of a file with a large header.
+# This is line 74 of a file with a large header.
+# This is line 75 of a file with a large header.
+# This is line 76 of a file with a large header.
+# This is line 77 of a file with a large header.
+# This is line 78 of a file with a large header.
+# This is line 79 of a file with a large header.
+# This is line 80 of a file with a large header.
+# This is line 81 of a file with a large header.
+# This is line 82 of a file with a large header.
+# This is line 83 of a file with a large header.
+# This is line 84 of a file with a large header.
+# This is line 85 of a file with a large header.
+# This is line 86 of a file with a large header.
+# This is line 87 of a file with a large header.
+# This is line 88 of a file with a large header.
+# This is line 89 of a file with a large header.
+# This is line 90 of a file with a large header.
+# This is line 91 of a file with a large header.
+# This is line 92 of a file with a large header.
+# This is line 93 of a file with a large header.
+# This is line 94 of a file with a large header.
+# This is line 95 of a file with a large header.
+# This is line 96 of a file with a large header.
+# This is line 97 of a file with a large header.
+# This is line 98 of a file with a large header.
+# This is line 99 of a file with a large header.
+# This is line 100 of a file with a large header.
+# This is line 101 of a file with a large header.
+# This is line 102 of a file with a large header.
+# This is line 103 of a file with a large header.
+# This is line 104 of a file with a large header.
+# This is line 105 of a file with a large header.
+# This is line 106 of a file with a large header.
+# This is line 107 of a file with a large header.
+# This is line 108 of a file with a large header.
+# This is line 109 of a file with a large header.
+# This is line 110 of a file with a large header.
+# This is line 111 of a file with a large header.
+# This is line 112 of a file with a large header.
+# This is line 113 of a file with a large header.
+# This is line 114 of a file with a large header.
+# This is line 115 of a file with a large header.
+# This is line 116 of a file with a large header.
+# This is line 117 of a file with a large header.
+# This is line 118 of a file with a large header.
+# This is line 119 of a file with a large header.
+# This is line 120 of a file with a large header.
+# This is line 121 of a file with a large header.
+# This is line 122 of a file with a large header.
+# This is line 123 of a file with a large header.
+# This is line 124 of a file with a large header.
+# This is line 125 of a file with a large header.
+# This is line 126 of a file with a large header.
+# This is line 127 of a file with a large header.
+# This is line 128 of a file with a large header.
+# This is line 129 of a file with a large header.
+# This is line 130 of a file with a large header.
+# This is line 131 of a file with a large header.
+# This is line 132 of a file with a large header.
+# This is line 133 of a file with a large header.
+# This is line 134 of a file with a large header.
+# This is line 135 of a file with a large header.
+# This is line 136 of a file with a large header.
+# This is line 137 of a file with a large header.
+# This is line 138 of a file with a large header.
+# This is line 139 of a file with a large header.
+# This is line 140 of a file with a large header.
+# This is line 141 of a file with a large header.
+# This is line 142 of a file with a large header.
+# This is line 143 of a file with a large header.
+# This is line 144 of a file with a large header.
+# This is line 145 of a file with a large header.
+# This is line 146 of a file with a large header.
+# This is line 147 of a file with a large header.
+# This is line 148 of a file with a large header.
+# This is line 149 of a file with a large header.
+# This is line 150 of a file with a large header.
+# This is line 151 of a file with a large header.
+# This is line 152 of a file with a large header.
+# This is line 153 of a file with a large header.
+# This is line 154 of a file with a large header.
+# This is line 155 of a file with a large header.
+# This is line 156 of a file with a large header.
+# This is line 157 of a file with a large header.
+# This is line 158 of a file with a large header.
+# This is line 159 of a file with a large header.
+# This is line 160 of a file with a large header.
+# This is line 161 of a file with a large header.
+# This is line 162 of a file with a large header.
+# This is line 163 of a file with a large header.
+# This is line 164 of a file with a large header.
+# This is line 165 of a file with a large header.
+# This is line 166 of a file with a large header.
+# This is line 167 of a file with a large header.
+# This is line 168 of a file with a large header.
+# This is line 169 of a file with a large header.
+# This is line 170 of a file with a large header.
+# This is line 171 of a file with a large header.
+# This is line 172 of a file with a large header.
+# This is line 173 of a file with a large header.
+# This is line 174 of a file with a large header.
+# This is line 175 of a file with a large header.
+# This is line 176 of a file with a large header.
+# This is line 177 of a file with a large header.
+# This is line 178 of a file with a large header.
+# This is line 179 of a file with a large header.
+# This is line 180 of a file with a large header.
+# This is line 181 of a file with a large header.
+# This is line 182 of a file with a large header.
+# This is line 183 of a file with a large header.
+# This is line 184 of a file with a large header.
+# This is line 185 of a file with a large header.
+# This is line 186 of a file with a large header.
+# This is line 187 of a file with a large header.
+# This is line 188 of a file with a large header.
+# This is line 189 of a file with a large header.
+# This is line 190 of a file with a large header.
+# This is line 191 of a file with a large header.
+# This is line 192 of a file with a large header.
+# This is line 193 of a file with a large header.
+# This is line 194 of a file with a large header.
+# This is line 195 of a file with a large header.
+# This is line 196 of a file with a large header.
+# This is line 197 of a file with a large header.
+# This is line 198 of a file with a large header.
+# This is line 199 of a file with a large header.
+# This is line 200 of a file with a large header.
+# This is line 201 of a file with a large header.
+# This is line 202 of a file with a large header.
+# This is line 203 of a file with a large header.
+# This is line 204 of a file with a large header.
+# This is line 205 of a file with a large header.
+# This is line 206 of a file with a large header.
+# This is line 207 of a file with a large header.
+# This is line 208 of a file with a large header.
+# This is line 209 of a file with a large header.
+# This is line 210 of a file with a large header.
+# This is line 211 of a file with a large header.
+# This is line 212 of a file with a large header.
+# This is line 213 of a file with a large header.
+# This is line 214 of a file with a large header.
+# This is line 215 of a file with a large header.
+# This is line 216 of a file with a large header.
+# This is line 217 of a file with a large header.
+# This is line 218 of a file with a large header.
+# This is line 219 of a file with a large header.
+# This is line 220 of a file with a large header.
+# This is line 221 of a file with a large header.
+# This is line 222 of a file with a large header.
+# This is line 223 of a file with a large header.
+# This is line 224 of a file with a large header.
+# This is line 225 of a file with a large header.
+# This is line 226 of a file with a large header.
+# This is line 227 of a file with a large header.
+# This is line 228 of a file with a large header.
+# This is line 229 of a file with a large header.
+# This is line 230 of a file with a large header.
+# This is line 231 of a file with a large header.
+# This is line 232 of a file with a large header.
+# This is line 233 of a file with a large header.
+# This is line 234 of a file with a large header.
+# This is line 235 of a file with a large header.
+# This is line 236 of a file with a large header.
+# This is line 237 of a file with a large header.
+# This is line 238 of a file with a large header.
+# This is line 239 of a file with a large header.
+# This is line 240 of a file with a large header.
+# This is line 241 of a file with a large header.
+# This is line 242 of a file with a large header.
+# This is line 243 of a file with a large header.
+# This is line 244 of a file with a large header.
+# This is line 245 of a file with a large header.
+# This is line 246 of a file with a large header.
+# This is line 247 of a file with a large header.
+# This is line 248 of a file with a large header.
+# This is line 249 of a file with a large header.
+# This is line 250 of a file with a large header.
+# This is line 251 of a file with a large header.
+# This is line 252 of a file with a large header.
+# This is line 253 of a file with a large header.
+# This is line 254 of a file with a large header.
+# This is line 255 of a file with a large header.
+# This is line 256 of a file with a large header.
+# This is line 257 of a file with a large header.
+# This is line 258 of a file with a large header.
+# This is line 259 of a file with a large header.
+# This is line 260 of a file with a large header.
+# This is line 261 of a file with a large header.
+# This is line 262 of a file with a large header.
+# This is line 263 of a file with a large header.
+# This is line 264 of a file with a large header.
+# This is line 265 of a file with a large header.
+# This is line 266 of a file with a large header.
+# This is line 267 of a file with a large header.
+# This is line 268 of a file with a large header.
+# This is line 269 of a file with a large header.
+# This is line 270 of a file with a large header.
+# This is line 271 of a file with a large header.
+# This is line 272 of a file with a large header.
+# This is line 273 of a file with a large header.
+# This is line 274 of a file with a large header.
+# This is line 275 of a file with a large header.
+# This is line 276 of a file with a large header.
+# This is line 277 of a file with a large header.
+# This is line 278 of a file with a large header.
+# This is line 279 of a file with a large header.
+# This is line 280 of a file with a large header.
+# This is line 281 of a file with a large header.
+# This is line 282 of a file with a large header.
+# This is line 283 of a file with a large header.
+# This is line 284 of a file with a large header.
+# This is line 285 of a file with a large header.
+# This is line 286 of a file with a large header.
+# This is line 287 of a file with a large header.
+# This is line 288 of a file with a large header.
+# This is line 289 of a file with a large header.
+# This is line 290 of a file with a large header.
+# This is line 291 of a file with a large header.
+# This is line 292 of a file with a large header.
+# This is line 293 of a file with a large header.
+# This is line 294 of a file with a large header.
+# This is line 295 of a file with a large header.
+# This is line 296 of a file with a large header.
+# This is line 297 of a file with a large header.
+# This is line 298 of a file with a large header.
+# This is line 299 of a file with a large header.
+# This is line 300 of a file with a large header.
+# This is line 301 of a file with a large header.
+# This is line 302 of a file with a large header.
+# This is line 303 of a file with a large header.
+# This is line 304 of a file with a large header.
+# This is line 305 of a file with a large header.
+# This is line 306 of a file with a large header.
+# This is line 307 of a file with a large header.
+# This is line 308 of a file with a large header.
+# This is line 309 of a file with a large header.
+# This is line 310 of a file with a large header.
+# This is line 311 of a file with a large header.
+# This is line 312 of a file with a large header.
+# This is line 313 of a file with a large header.
+# This is line 314 of a file with a large header.
+# This is line 315 of a file with a large header.
+# This is line 316 of a file with a large header.
+# This is line 317 of a file with a large header.
+# This is line 318 of a file with a large header.
+# This is line 319 of a file with a large header.
+# This is line 320 of a file with a large header.
+# This is line 321 of a file with a large header.
+# This is line 322 of a file with a large header.
+# This is line 323 of a file with a large header.
+# This is line 324 of a file with a large header.
+# This is line 325 of a file with a large header.
+# This is line 326 of a file with a large header.
+# This is line 327 of a file with a large header.
+# This is line 328 of a file with a large header.
+# This is line 329 of a file with a large header.
+# This is line 330 of a file with a large header.
+# This is line 331 of a file with a large header.
+# This is line 332 of a file with a large header.
+# This is line 333 of a file with a large header.
+# This is line 334 of a file with a large header.
+# This is line 335 of a file with a large header.
+# This is line 336 of a file with a large header.
+# This is line 337 of a file with a large header.
+# This is line 338 of a file with a large header.
+# This is line 339 of a file with a large header.
+# This is line 340 of a file with a large header.
+# This is line 341 of a file with a large header.
+# This is line 342 of a file with a large header.
+# This is line 343 of a file with a large header.
+# This is line 344 of a file with a large header.
+# This is line 345 of a file with a large header.
+# This is line 346 of a file with a large header.
+# This is line 347 of a file with a large header.
+# This is line 348 of a file with a large header.
+# This is line 349 of a file with a large header.
+# This is line 350 of a file with a large header.
+# This is line 351 of a file with a large header.
+# This is line 352 of a file with a large header.
+# This is line 353 of a file with a large header.
+# This is line 354 of a file with a large header.
+# This is line 355 of a file with a large header.
+# This is line 356 of a file with a large header.
+# This is line 357 of a file with a large header.
+# This is line 358 of a file with a large header.
+# This is line 359 of a file with a large header.
+# This is line 360 of a file with a large header.
+# This is line 361 of a file with a large header.
+# This is line 362 of a file with a large header.
+# This is line 363 of a file with a large header.
+# This is line 364 of a file with a large header.
+# This is line 365 of a file with a large header.
+# This is line 366 of a file with a large header.
+# This is line 367 of a file with a large header.
+# This is line 368 of a file with a large header.
+# This is line 369 of a file with a large header.
+# This is line 370 of a file with a large header.
+# This is line 371 of a file with a large header.
+# This is line 372 of a file with a large header.
+# This is line 373 of a file with a large header.
+# This is line 374 of a file with a large header.
+# This is line 375 of a file with a large header.
+# This is line 376 of a file with a large header.
+# This is line 377 of a file with a large header.
+# This is line 378 of a file with a large header.
+# This is line 379 of a file with a large header.
+# This is line 380 of a file with a large header.
+# This is line 381 of a file with a large header.
+# This is line 382 of a file with a large header.
+# This is line 383 of a file with a large header.
+# This is line 384 of a file with a large header.
+# This is line 385 of a file with a large header.
+# This is line 386 of a file with a large header.
+# This is line 387 of a file with a large header.
+# This is line 388 of a file with a large header.
+# This is line 389 of a file with a large header.
+# This is line 390 of a file with a large header.
+# This is line 391 of a file with a large header.
+# This is line 392 of a file with a large header.
+# This is line 393 of a file with a large header.
+# This is line 394 of a file with a large header.
+# This is line 395 of a file with a large header.
+# This is line 396 of a file with a large header.
+# This is line 397 of a file with a large header.
+# This is line 398 of a file with a large header.
+# This is line 399 of a file with a large header.
+# This is line 400 of a file with a large header.
+# This is line 401 of a file with a large header.
+# This is line 402 of a file with a large header.
+# This is line 403 of a file with a large header.
+# This is line 404 of a file with a large header.
+# This is line 405 of a file with a large header.
+# This is line 406 of a file with a large header.
+# This is line 407 of a file with a large header.
+# This is line 408 of a file with a large header.
+# This is line 409 of a file with a large header.
+# This is line 410 of a file with a large header.
+# This is line 411 of a file with a large header.
+# This is line 412 of a file with a large header.
+# This is line 413 of a file with a large header.
+# This is line 414 of a file with a large header.
+# This is line 415 of a file with a large header.
+# This is line 416 of a file with a large header.
+# This is line 417 of a file with a large header.
+# This is line 418 of a file with a large header.
+# This is line 419 of a file with a large header.
+# This is line 420 of a file with a large header.
+# This is line 421 of a file with a large header.
+# This is line 422 of a file with a large header.
+# This is line 423 of a file with a large header.
+# This is line 424 of a file with a large header.
+# This is line 425 of a file with a large header.
+# This is line 426 of a file with a large header.
+# This is line 427 of a file with a large header.
+# This is line 428 of a file with a large header.
+# This is line 429 of a file with a large header.
+# This is line 430 of a file with a large header.
+# This is line 431 of a file with a large header.
+# This is line 432 of a file with a large header.
+# This is line 433 of a file with a large header.
+# This is line 434 of a file with a large header.
+# This is line 435 of a file with a large header.
+# This is line 436 of a file with a large header.
+# This is line 437 of a file with a large header.
+# This is line 438 of a file with a large header.
+# This is line 439 of a file with a large header.
+# This is line 440 of a file with a large header.
+# This is line 441 of a file with a large header.
+# This is line 442 of a file with a large header.
+# This is line 443 of a file with a large header.
+# This is line 444 of a file with a large header.
+# This is line 445 of a file with a large header.
+# This is line 446 of a file with a large header.
+# This is line 447 of a file with a large header.
+# This is line 448 of a file with a large header.
+# This is line 449 of a file with a large header.
+# This is line 450 of a file with a large header.
+# This is line 451 of a file with a large header.
+# This is line 452 of a file with a large header.
+# This is line 453 of a file with a large header.
+# This is line 454 of a file with a large header.
+# This is line 455 of a file with a large header.
+# This is line 456 of a file with a large header.
+# This is line 457 of a file with a large header.
+# This is line 458 of a file with a large header.
+# This is line 459 of a file with a large header.
+# This is line 460 of a file with a large header.
+# This is line 461 of a file with a large header.
+# This is line 462 of a file with a large header.
+# This is line 463 of a file with a large header.
+# This is line 464 of a file with a large header.
+# This is line 465 of a file with a large header.
+# This is line 466 of a file with a large header.
+# This is line 467 of a file with a large header.
+# This is line 468 of a file with a large header.
+# This is line 469 of a file with a large header.
+# This is line 470 of a file with a large header.
+# This is line 471 of a file with a large header.
+# This is line 472 of a file with a large header.
+# This is line 473 of a file with a large header.
+# This is line 474 of a file with a large header.
+# This is line 475 of a file with a large header.
+# This is line 476 of a file with a large header.
+# This is line 477 of a file with a large header.
+# This is line 478 of a file with a large header.
+# This is line 479 of a file with a large header.
+# This is line 480 of a file with a large header.
+# This is line 481 of a file with a large header.
+# This is line 482 of a file with a large header.
+# This is line 483 of a file with a large header.
+# This is line 484 of a file with a large header.
+# This is line 485 of a file with a large header.
+# This is line 486 of a file with a large header.
+# This is line 487 of a file with a large header.
+# This is line 488 of a file with a large header.
+# This is line 489 of a file with a large header.
+# This is line 490 of a file with a large header.
+# This is line 491 of a file with a large header.
+# This is line 492 of a file with a large header.
+# This is line 493 of a file with a large header.
+# This is line 494 of a file with a large header.
+# This is line 495 of a file with a large header.
+# This is line 496 of a file with a large header.
+# This is line 497 of a file with a large header.
+# This is line 498 of a file with a large header.
+# This is line 499 of a file with a large header.
+# This is line 500 of a file with a large header.
+# This is line 501 of a file with a large header.
+# This is line 502 of a file with a large header.
+# This is line 503 of a file with a large header.
+# This is line 504 of a file with a large header.
+# This is line 505 of a file with a large header.
+# This is line 506 of a file with a large header.
+# This is line 507 of a file with a large header.
+# This is line 508 of a file with a large header.
+# This is line 509 of a file with a large header.
+# This is line 510 of a file with a large header.
+# This is line 511 of a file with a large header.
+# This is line 512 of a file with a large header.
+# This is line 513 of a file with a large header.
+# This is line 514 of a file with a large header.
+# This is line 515 of a file with a large header.
+# This is line 516 of a file with a large header.
+# This is line 517 of a file with a large header.
+# This is line 518 of a file with a large header.
+# This is line 519 of a file with a large header.
+# This is line 520 of a file with a large header.
+# This is line 521 of a file with a large header.
+# This is line 522 of a file with a large header.
+# This is line 523 of a file with a large header.
+# This is line 524 of a file with a large header.
+# This is line 525 of a file with a large header.
+# This is line 526 of a file with a large header.
+# This is line 527 of a file with a large header.
+# This is line 528 of a file with a large header.
+# This is line 529 of a file with a large header.
+# This is line 530 of a file with a large header.
+# This is line 531 of a file with a large header.
+# This is line 532 of a file with a large header.
+# This is line 533 of a file with a large header.
+# This is line 534 of a file with a large header.
+# This is line 535 of a file with a large header.
+# This is line 536 of a file with a large header.
+# This is line 537 of a file with a large header.
+# This is line 538 of a file with a large header.
+# This is line 539 of a file with a large header.
+# This is line 540 of a file with a large header.
+# This is line 541 of a file with a large header.
+# This is line 542 of a file with a large header.
+# This is line 543 of a file with a large header.
+# This is line 544 of a file with a large header.
+# This is line 545 of a file with a large header.
+# This is line 546 of a file with a large header.
+# This is line 547 of a file with a large header.
+# This is line 548 of a file with a large header.
+# This is line 549 of a file with a large header.
+# This is line 550 of a file with a large header.
+# This is line 551 of a file with a large header.
+# This is line 552 of a file with a large header.
+# This is line 553 of a file with a large header.
+# This is line 554 of a file with a large header.
+# This is line 555 of a file with a large header.
+# This is line 556 of a file with a large header.
+# This is line 557 of a file with a large header.
+# This is line 558 of a file with a large header.
+# This is line 559 of a file with a large header.
+# This is line 560 of a file with a large header.
+# This is line 561 of a file with a large header.
+# This is line 562 of a file with a large header.
+# This is line 563 of a file with a large header.
+# This is line 564 of a file with a large header.
+# This is line 565 of a file with a large header.
+# This is line 566 of a file with a large header.
+# This is line 567 of a file with a large header.
+# This is line 568 of a file with a large header.
+# This is line 569 of a file with a large header.
+# This is line 570 of a file with a large header.
+# This is line 571 of a file with a large header.
+# This is line 572 of a file with a large header.
+# This is line 573 of a file with a large header.
+# This is line 574 of a file with a large header.
+# This is line 575 of a file with a large header.
+# This is line 576 of a file with a large header.
+# This is line 577 of a file with a large header.
+# This is line 578 of a file with a large header.
+# This is line 579 of a file with a large header.
+# This is line 580 of a file with a large header.
+# This is line 581 of a file with a large header.
+# This is line 582 of a file with a large header.
+# This is line 583 of a file with a large header.
+# This is line 584 of a file with a large header.
+# This is line 585 of a file with a large header.
+# This is line 586 of a file with a large header.
+# This is line 587 of a file with a large header.
+# This is line 588 of a file with a large header.
+# This is line 589 of a file with a large header.
+# This is line 590 of a file with a large header.
+# This is line 591 of a file with a large header.
+# This is line 592 of a file with a large header.
+# This is line 593 of a file with a large header.
+# This is line 594 of a file with a large header.
+# This is line 595 of a file with a large header.
+# This is line 596 of a file with a large header.
+# This is line 597 of a file with a large header.
+# This is line 598 of a file with a large header.
+# This is line 599 of a file with a large header.
+# This is line 600 of a file with a large header.
+# This is line 601 of a file with a large header.
+# This is line 602 of a file with a large header.
+# This is line 603 of a file with a large header.
+# This is line 604 of a file with a large header.
+# This is line 605 of a file with a large header.
+# This is line 606 of a file with a large header.
+# This is line 607 of a file with a large header.
+# This is line 608 of a file with a large header.
+# This is line 609 of a file with a large header.
+# This is line 610 of a file with a large header.
+# This is line 611 of a file with a large header.
+# This is line 612 of a file with a large header.
+# This is line 613 of a file with a large header.
+# This is line 614 of a file with a large header.
+# This is line 615 of a file with a large header.
+# This is line 616 of a file with a large header.
+# This is line 617 of a file with a large header.
+# This is line 618 of a file with a large header.
+# This is line 619 of a file with a large header.
+# This is line 620 of a file with a large header.
+# This is line 621 of a file with a large header.
+# This is line 622 of a file with a large header.
+# This is line 623 of a file with a large header.
+# This is line 624 of a file with a large header.
+# This is line 625 of a file with a large header.
+# This is line 626 of a file with a large header.
+# This is line 627 of a file with a large header.
+# This is line 628 of a file with a large header.
+# This is line 629 of a file with a large header.
+# This is line 630 of a file with a large header.
+# This is line 631 of a file with a large header.
+# This is line 632 of a file with a large header.
+# This is line 633 of a file with a large header.
+# This is line 634 of a file with a large header.
+# This is line 635 of a file with a large header.
+# This is line 636 of a file with a large header.
+# This is line 637 of a file with a large header.
+# This is line 638 of a file with a large header.
+# This is line 639 of a file with a large header.
+# This is line 640 of a file with a large header.
+# This is line 641 of a file with a large header.
+# This is line 642 of a file with a large header.
+# This is line 643 of a file with a large header.
+# This is line 644 of a file with a large header.
+# This is line 645 of a file with a large header.
+# This is line 646 of a file with a large header.
+# This is line 647 of a file with a large header.
+# This is line 648 of a file with a large header.
+# This is line 649 of a file with a large header.
+# This is line 650 of a file with a large header.
+# This is line 651 of a file with a large header.
+# This is line 652 of a file with a large header.
+# This is line 653 of a file with a large header.
+# This is line 654 of a file with a large header.
+# This is line 655 of a file with a large header.
+# This is line 656 of a file with a large header.
+# This is line 657 of a file with a large header.
+# This is line 658 of a file with a large header.
+# This is line 659 of a file with a large header.
+# This is line 660 of a file with a large header.
+# This is line 661 of a file with a large header.
+# This is line 662 of a file with a large header.
+# This is line 663 of a file with a large header.
+# This is line 664 of a file with a large header.
+# This is line 665 of a file with a large header.
+# This is line 666 of a file with a large header.
+# This is line 667 of a file with a large header.
+# This is line 668 of a file with a large header.
+# This is line 669 of a file with a large header.
+# This is line 670 of a file with a large header.
+# This is line 671 of a file with a large header.
+# This is line 672 of a file with a large header.
+# This is line 673 of a file with a large header.
+# This is line 674 of a file with a large header.
+# This is line 675 of a file with a large header.
+# This is line 676 of a file with a large header.
+# This is line 677 of a file with a large header.
+# This is line 678 of a file with a large header.
+# This is line 679 of a file with a large header.
+# This is line 680 of a file with a large header.
+# This is line 681 of a file with a large header.
+# This is line 682 of a file with a large header.
+# This is line 683 of a file with a large header.
+# This is line 684 of a file with a large header.
+# This is line 685 of a file with a large header.
+# This is line 686 of a file with a large header.
+# This is line 687 of a file with a large header.
+# This is line 688 of a file with a large header.
+# This is line 689 of a file with a large header.
+# This is line 690 of a file with a large header.
+# This is line 691 of a file with a large header.
+# This is line 692 of a file with a large header.
+# This is line 693 of a file with a large header.
+# This is line 694 of a file with a large header.
+# This is line 695 of a file with a large header.
+# This is line 696 of a file with a large header.
+# This is line 697 of a file with a large header.
+# This is line 698 of a file with a large header.
+# This is line 699 of a file with a large header.
+# This is line 700 of a file with a large header.
+# This is line 701 of a file with a large header.
+# This is line 702 of a file with a large header.
+# This is line 703 of a file with a large header.
+# This is line 704 of a file with a large header.
+# This is line 705 of a file with a large header.
+# This is line 706 of a file with a large header.
+# This is line 707 of a file with a large header.
+# This is line 708 of a file with a large header.
+# This is line 709 of a file with a large header.
+# This is line 710 of a file with a large header.
+# This is line 711 of a file with a large header.
+# This is line 712 of a file with a large header.
+# This is line 713 of a file with a large header.
+# This is line 714 of a file with a large header.
+# This is line 715 of a file with a large header.
+# This is line 716 of a file with a large header.
+# This is line 717 of a file with a large header.
+# This is line 718 of a file with a large header.
+# This is line 719 of a file with a large header.
+# This is line 720 of a file with a large header.
+# This is line 721 of a file with a large header.
+# This is line 722 of a file with a large header.
+# This is line 723 of a file with a large header.
+# This is line 724 of a file with a large header.
+# This is line 725 of a file with a large header.
+# This is line 726 of a file with a large header.
+# This is line 727 of a file with a large header.
+# This is line 728 of a file with a large header.
+# This is line 729 of a file with a large header.
+# This is line 730 of a file with a large header.
+# This is line 731 of a file with a large header.
+# This is line 732 of a file with a large header.
+# This is line 733 of a file with a large header.
+# This is line 734 of a file with a large header.
+# This is line 735 of a file with a large header.
+# This is line 736 of a file with a large header.
+# This is line 737 of a file with a large header.
+# This is line 738 of a file with a large header.
+# This is line 739 of a file with a large header.
+# This is line 740 of a file with a large header.
+# This is line 741 of a file with a large header.
+# This is line 742 of a file with a large header.
+# This is line 743 of a file with a large header.
+# This is line 744 of a file with a large header.
+# This is line 745 of a file with a large header.
+# This is line 746 of a file with a large header.
+# This is line 747 of a file with a large header.
+# This is line 748 of a file with a large header.
+# This is line 749 of a file with a large header.
+# This is line 750 of a file with a large header.
+# This is line 751 of a file with a large header.
+# This is line 752 of a file with a large header.
+# This is line 753 of a file with a large header.
+# This is line 754 of a file with a large header.
+# This is line 755 of a file with a large header.
+# This is line 756 of a file with a large header.
+# This is line 757 of a file with a large header.
+# This is line 758 of a file with a large header.
+# This is line 759 of a file with a large header.
+# This is line 760 of a file with a large header.
+# This is line 761 of a file with a large header.
+# This is line 762 of a file with a large header.
+# This is line 763 of a file with a large header.
+# This is line 764 of a file with a large header.
+# This is line 765 of a file with a large header.
+# This is line 766 of a file with a large header.
+# This is line 767 of a file with a large header.
+# This is line 768 of a file with a large header.
+# This is line 769 of a file with a large header.
+# This is line 770 of a file with a large header.
+# This is line 771 of a file with a large header.
+# This is line 772 of a file with a large header.
+# This is line 773 of a file with a large header.
+# This is line 774 of a file with a large header.
+# This is line 775 of a file with a large header.
+# This is line 776 of a file with a large header.
+# This is line 777 of a file with a large header.
+# This is line 778 of a file with a large header.
+# This is line 779 of a file with a large header.
+# This is line 780 of a file with a large header.
+# This is line 781 of a file with a large header.
+# This is line 782 of a file with a large header.
+# This is line 783 of a file with a large header.
+# This is line 784 of a file with a large header.
+# This is line 785 of a file with a large header.
+# This is line 786 of a file with a large header.
+# This is line 787 of a file with a large header.
+# This is line 788 of a file with a large header.
+# This is line 789 of a file with a large header.
+# This is line 790 of a file with a large header.
+# This is line 791 of a file with a large header.
+# This is line 792 of a file with a large header.
+# This is line 793 of a file with a large header.
+# This is line 794 of a file with a large header.
+# This is line 795 of a file with a large header.
+# This is line 796 of a file with a large header.
+# This is line 797 of a file with a large header.
+# This is line 798 of a file with a large header.
+# This is line 799 of a file with a large header.
+# This is line 800 of a file with a large header.
+# This is line 801 of a file with a large header.
+# This is line 802 of a file with a large header.
+# This is line 803 of a file with a large header.
+# This is line 804 of a file with a large header.
+# This is line 805 of a file with a large header.
+# This is line 806 of a file with a large header.
+# This is line 807 of a file with a large header.
+# This is line 808 of a file with a large header.
+# This is line 809 of a file with a large header.
+# This is line 810 of a file with a large header.
+# This is line 811 of a file with a large header.
+# This is line 812 of a file with a large header.
+# This is line 813 of a file with a large header.
+# This is line 814 of a file with a large header.
+# This is line 815 of a file with a large header.
+# This is line 816 of a file with a large header.
+# This is line 817 of a file with a large header.
+# This is line 818 of a file with a large header.
+# This is line 819 of a file with a large header.
+# This is line 820 of a file with a large header.
+# This is line 821 of a file with a large header.
+# This is line 822 of a file with a large header.
+# This is line 823 of a file with a large header.
+# This is line 824 of a file with a large header.
+# This is line 825 of a file with a large header.
+# This is line 826 of a file with a large header.
+# This is line 827 of a file with a large header.
+# This is line 828 of a file with a large header.
+# This is line 829 of a file with a large header.
+# This is line 830 of a file with a large header.
+# This is line 831 of a file with a large header.
+# This is line 832 of a file with a large header.
+# This is line 833 of a file with a large header.
+# This is line 834 of a file with a large header.
+# This is line 835 of a file with a large header.
+# This is line 836 of a file with a large header.
+# This is line 837 of a file with a large header.
+# This is line 838 of a file with a large header.
+# This is line 839 of a file with a large header.
+# This is line 840 of a file with a large header.
+# This is line 841 of a file with a large header.
+# This is line 842 of a file with a large header.
+# This is line 843 of a file with a large header.
+# This is line 844 of a file with a large header.
+# This is line 845 of a file with a large header.
+# This is line 846 of a file with a large header.
+# This is line 847 of a file with a large header.
+# This is line 848 of a file with a large header.
+# This is line 849 of a file with a large header.
+# This is line 850 of a file with a large header.
+# This is line 851 of a file with a large header.
+# This is line 852 of a file with a large header.
+# This is line 853 of a file with a large header.
+# This is line 854 of a file with a large header.
+# This is line 855 of a file with a large header.
+# This is line 856 of a file with a large header.
+# This is line 857 of a file with a large header.
+# This is line 858 of a file with a large header.
+# This is line 859 of a file with a large header.
+# This is line 860 of a file with a large header.
+# This is line 861 of a file with a large header.
+# This is line 862 of a file with a large header.
+# This is line 863 of a file with a large header.
+# This is line 864 of a file with a large header.
+# This is line 865 of a file with a large header.
+# This is line 866 of a file with a large header.
+# This is line 867 of a file with a large header.
+# This is line 868 of a file with a large header.
+# This is line 869 of a file with a large header.
+# This is line 870 of a file with a large header.
+# This is line 871 of a file with a large header.
+# This is line 872 of a file with a large header.
+# This is line 873 of a file with a large header.
+# This is line 874 of a file with a large header.
+# This is line 875 of a file with a large header.
+# This is line 876 of a file with a large header.
+# This is line 877 of a file with a large header.
+# This is line 878 of a file with a large header.
+# This is line 879 of a file with a large header.
+# This is line 880 of a file with a large header.
+# This is line 881 of a file with a large header.
+# This is line 882 of a file with a large header.
+# This is line 883 of a file with a large header.
+# This is line 884 of a file with a large header.
+# This is line 885 of a file with a large header.
+# This is line 886 of a file with a large header.
+# This is line 887 of a file with a large header.
+# This is line 888 of a file with a large header.
+# This is line 889 of a file with a large header.
+# This is line 890 of a file with a large header.
+# This is line 891 of a file with a large header.
+# This is line 892 of a file with a large header.
+# This is line 893 of a file with a large header.
+# This is line 894 of a file with a large header.
+# This is line 895 of a file with a large header.
+# This is line 896 of a file with a large header.
+# This is line 897 of a file with a large header.
+# This is line 898 of a file with a large header.
+# This is line 899 of a file with a large header.
+# This is line 900 of a file with a large header.
+# This is line 901 of a file with a large header.
+# This is line 902 of a file with a large header.
+# This is line 903 of a file with a large header.
+# This is line 904 of a file with a large header.
+# This is line 905 of a file with a large header.
+# This is line 906 of a file with a large header.
+# This is line 907 of a file with a large header.
+# This is line 908 of a file with a large header.
+# This is line 909 of a file with a large header.
+# This is line 910 of a file with a large header.
+# This is line 911 of a file with a large header.
+# This is line 912 of a file with a large header.
+# This is line 913 of a file with a large header.
+# This is line 914 of a file with a large header.
+# This is line 915 of a file with a large header.
+# This is line 916 of a file with a large header.
+# This is line 917 of a file with a large header.
+# This is line 918 of a file with a large header.
+# This is line 919 of a file with a large header.
+# This is line 920 of a file with a large header.
+# This is line 921 of a file with a large header.
+# This is line 922 of a file with a large header.
+# This is line 923 of a file with a large header.
+# This is line 924 of a file with a large header.
+# This is line 925 of a file with a large header.
+# This is line 926 of a file with a large header.
+# This is line 927 of a file with a large header.
+# This is line 928 of a file with a large header.
+# This is line 929 of a file with a large header.
+# This is line 930 of a file with a large header.
+# This is line 931 of a file with a large header.
+# This is line 932 of a file with a large header.
+# This is line 933 of a file with a large header.
+# This is line 934 of a file with a large header.
+# This is line 935 of a file with a large header.
+# This is line 936 of a file with a large header.
+# This is line 937 of a file with a large header.
+# This is line 938 of a file with a large header.
+# This is line 939 of a file with a large header.
+# This is line 940 of a file with a large header.
+# This is line 941 of a file with a large header.
+# This is line 942 of a file with a large header.
+# This is line 943 of a file with a large header.
+# This is line 944 of a file with a large header.
+# This is line 945 of a file with a large header.
+# This is line 946 of a file with a large header.
+# This is line 947 of a file with a large header.
+# This is line 948 of a file with a large header.
+# This is line 949 of a file with a large header.
+# This is line 950 of a file with a large header.
+# This is line 951 of a file with a large header.
+# This is line 952 of a file with a large header.
+# This is line 953 of a file with a large header.
+# This is line 954 of a file with a large header.
+# This is line 955 of a file with a large header.
+# This is line 956 of a file with a large header.
+# This is line 957 of a file with a large header.
+# This is line 958 of a file with a large header.
+# This is line 959 of a file with a large header.
+# This is line 960 of a file with a large header.
+# This is line 961 of a file with a large header.
+# This is line 962 of a file with a large header.
+# This is line 963 of a file with a large header.
+# This is line 964 of a file with a large header.
+# This is line 965 of a file with a large header.
+# This is line 966 of a file with a large header.
+# This is line 967 of a file with a large header.
+# This is line 968 of a file with a large header.
+# This is line 969 of a file with a large header.
+# This is line 970 of a file with a large header.
+# This is line 971 of a file with a large header.
+# This is line 972 of a file with a large header.
+# This is line 973 of a file with a large header.
+# This is line 974 of a file with a large header.
+# This is line 975 of a file with a large header.
+# This is line 976 of a file with a large header.
+# This is line 977 of a file with a large header.
+# This is line 978 of a file with a large header.
+# This is line 979 of a file with a large header.
+# This is line 980 of a file with a large header.
+# This is line 981 of a file with a large header.
+# This is line 982 of a file with a large header.
+# This is line 983 of a file with a large header.
+# This is line 984 of a file with a large header.
+# This is line 985 of a file with a large header.
+# This is line 986 of a file with a large header.
+# This is line 987 of a file with a large header.
+# This is line 988 of a file with a large header.
+# This is line 989 of a file with a large header.
+# This is line 990 of a file with a large header.
+# This is line 991 of a file with a large header.
+# This is line 992 of a file with a large header.
+# This is line 993 of a file with a large header.
+# This is line 994 of a file with a large header.
+# This is line 995 of a file with a large header.
+# This is line 996 of a file with a large header.
+# This is line 997 of a file with a large header.
+# This is line 998 of a file with a large header.
+# This is line 999 of a file with a large header.
+# This is line 1000 of a file with a large header.
+# This is line 1001 of a file with a large header.
+# This is line 1002 of a file with a large header.
+# This is line 1003 of a file with a large header.
+# This is line 1004 of a file with a large header.
+# This is line 1005 of a file with a large header.
+# This is line 1006 of a file with a large header.
+# This is line 1007 of a file with a large header.
+# This is line 1008 of a file with a large header.
+# This is line 1009 of a file with a large header.
+# This is line 1010 of a file with a large header.
+# This is line 1011 of a file with a large header.
+# This is line 1012 of a file with a large header.
+# This is line 1013 of a file with a large header.
+# This is line 1014 of a file with a large header.
+# This is line 1015 of a file with a large header.
+# This is line 1016 of a file with a large header.
+# This is line 1017 of a file with a large header.
+# This is line 1018 of a file with a large header.
+# This is line 1019 of a file with a large header.
+# This is line 1020 of a file with a large header.
+# This is line 1021 of a file with a large header.
+# This is line 1022 of a file with a large header.
+# This is line 1023 of a file with a large header.
+# This is line 1024 of a file with a large header.
+# This is line 1025 of a file with a large header.
+# This is line 1026 of a file with a large header.
+# This is line 1027 of a file with a large header.
+# This is line 1028 of a file with a large header.
+# This is line 1029 of a file with a large header.
+# This is line 1030 of a file with a large header.
+# This is line 1031 of a file with a large header.
+# This is line 1032 of a file with a large header.
+# This is line 1033 of a file with a large header.
+# This is line 1034 of a file with a large header.
+# This is line 1035 of a file with a large header.
+# This is line 1036 of a file with a large header.
+# This is line 1037 of a file with a large header.
+# This is line 1038 of a file with a large header.
+# This is line 1039 of a file with a large header.
+# This is line 1040 of a file with a large header.
+# This is line 1041 of a file with a large header.
+# This is line 1042 of a file with a large header.
+# This is line 1043 of a file with a large header.
+# This is line 1044 of a file with a large header.
+# This is line 1045 of a file with a large header.
+# This is line 1046 of a file with a large header.
+# This is line 1047 of a file with a large header.
+# This is line 1048 of a file with a large header.
+# This is line 1049 of a file with a large header.
+# This is line 1050 of a file with a large header.
+# This is line 1051 of a file with a large header.
+# This is line 1052 of a file with a large header.
+# This is line 1053 of a file with a large header.
+# This is line 1054 of a file with a large header.
+# This is line 1055 of a file with a large header.
+# This is line 1056 of a file with a large header.
+# This is line 1057 of a file with a large header.
+# This is line 1058 of a file with a large header.
+# This is line 1059 of a file with a large header.
+# This is line 1060 of a file with a large header.
+# This is line 1061 of a file with a large header.
+# This is line 1062 of a file with a large header.
+# This is line 1063 of a file with a large header.
+# This is line 1064 of a file with a large header.
+# This is line 1065 of a file with a large header.
+# This is line 1066 of a file with a large header.
+# This is line 1067 of a file with a large header.
+# This is line 1068 of a file with a large header.
+# This is line 1069 of a file with a large header.
+# This is line 1070 of a file with a large header.
+# This is line 1071 of a file with a large header.
+# This is line 1072 of a file with a large header.
+# This is line 1073 of a file with a large header.
+# This is line 1074 of a file with a large header.
+# This is line 1075 of a file with a large header.
+# This is line 1076 of a file with a large header.
+# This is line 1077 of a file with a large header.
+# This is line 1078 of a file with a large header.
+# This is line 1079 of a file with a large header.
+# This is line 1080 of a file with a large header.
+# This is line 1081 of a file with a large header.
+# This is line 1082 of a file with a large header.
+# This is line 1083 of a file with a large header.
+# This is line 1084 of a file with a large header.
+# This is line 1085 of a file with a large header.
+# This is line 1086 of a file with a large header.
+# This is line 1087 of a file with a large header.
+# This is line 1088 of a file with a large header.
+# This is line 1089 of a file with a large header.
+# This is line 1090 of a file with a large header.
+# This is line 1091 of a file with a large header.
+# This is line 1092 of a file with a large header.
+# This is line 1093 of a file with a large header.
+# This is line 1094 of a file with a large header.
+# This is line 1095 of a file with a large header.
+# This is line 1096 of a file with a large header.
+# This is line 1097 of a file with a large header.
+# This is line 1098 of a file with a large header.
+# This is line 1099 of a file with a large header.
+# This is line 1100 of a file with a large header.
+# This is line 1101 of a file with a large header.
+# This is line 1102 of a file with a large header.
+# This is line 1103 of a file with a large header.
+# This is line 1104 of a file with a large header.
+# This is line 1105 of a file with a large header.
+# This is line 1106 of a file with a large header.
+# This is line 1107 of a file with a large header.
+# This is line 1108 of a file with a large header.
+# This is line 1109 of a file with a large header.
+# This is line 1110 of a file with a large header.
+# This is line 1111 of a file with a large header.
+# This is line 1112 of a file with a large header.
+# This is line 1113 of a file with a large header.
+# This is line 1114 of a file with a large header.
+# This is line 1115 of a file with a large header.
+# This is line 1116 of a file with a large header.
+# This is line 1117 of a file with a large header.
+# This is line 1118 of a file with a large header.
+# This is line 1119 of a file with a large header.
+# This is line 1120 of a file with a large header.
+# This is line 1121 of a file with a large header.
+# This is line 1122 of a file with a large header.
+# This is line 1123 of a file with a large header.
+# This is line 1124 of a file with a large header.
+# This is line 1125 of a file with a large header.
+# This is line 1126 of a file with a large header.
+# This is line 1127 of a file with a large header.
+# This is line 1128 of a file with a large header.
+# This is line 1129 of a file with a large header.
+# This is line 1130 of a file with a large header.
+# This is line 1131 of a file with a large header.
+# This is line 1132 of a file with a large header.
+# This is line 1133 of a file with a large header.
+# This is line 1134 of a file with a large header.
+# This is line 1135 of a file with a large header.
+# This is line 1136 of a file with a large header.
+# This is line 1137 of a file with a large header.
+# This is line 1138 of a file with a large header.
+# This is line 1139 of a file with a large header.
+# This is line 1140 of a file with a large header.
+# This is line 1141 of a file with a large header.
+# This is line 1142 of a file with a large header.
+# This is line 1143 of a file with a large header.
+# This is line 1144 of a file with a large header.
+# This is line 1145 of a file with a large header.
+# This is line 1146 of a file with a large header.
+# This is line 1147 of a file with a large header.
+# This is line 1148 of a file with a large header.
+# This is line 1149 of a file with a large header.
+# This is line 1150 of a file with a large header.
+# This is line 1151 of a file with a large header.
+# This is line 1152 of a file with a large header.
+# This is line 1153 of a file with a large header.
+# This is line 1154 of a file with a large header.
+# This is line 1155 of a file with a large header.
+# This is line 1156 of a file with a large header.
+# This is line 1157 of a file with a large header.
+# This is line 1158 of a file with a large header.
+# This is line 1159 of a file with a large header.
+# This is line 1160 of a file with a large header.
+# This is line 1161 of a file with a large header.
+# This is line 1162 of a file with a large header.
+# This is line 1163 of a file with a large header.
+# This is line 1164 of a file with a large header.
+# This is line 1165 of a file with a large header.
+# This is line 1166 of a file with a large header.
+# This is line 1167 of a file with a large header.
+# This is line 1168 of a file with a large header.
+# This is line 1169 of a file with a large header.
+# This is line 1170 of a file with a large header.
+# This is line 1171 of a file with a large header.
+# This is line 1172 of a file with a large header.
+# This is line 1173 of a file with a large header.
+# This is line 1174 of a file with a large header.
+# This is line 1175 of a file with a large header.
+# This is line 1176 of a file with a large header.
+# This is line 1177 of a file with a large header.
+# This is line 1178 of a file with a large header.
+# This is line 1179 of a file with a large header.
+# This is line 1180 of a file with a large header.
+# This is line 1181 of a file with a large header.
+# This is line 1182 of a file with a large header.
+# This is line 1183 of a file with a large header.
+# This is line 1184 of a file with a large header.
+# This is line 1185 of a file with a large header.
+# This is line 1186 of a file with a large header.
+# This is line 1187 of a file with a large header.
+# This is line 1188 of a file with a large header.
+# This is line 1189 of a file with a large header.
+# This is line 1190 of a file with a large header.
+# This is line 1191 of a file with a large header.
+# This is line 1192 of a file with a large header.
+# This is line 1193 of a file with a large header.
+# This is line 1194 of a file with a large header.
+# This is line 1195 of a file with a large header.
+# This is line 1196 of a file with a large header.
+# This is line 1197 of a file with a large header.
+# This is line 1198 of a file with a large header.
+# This is line 1199 of a file with a large header.
+# This is line 1200 of a file with a large header.
+# This is line 1201 of a file with a large header.
+# This is line 1202 of a file with a large header.
+# This is line 1203 of a file with a large header.
+# This is line 1204 of a file with a large header.
+# This is line 1205 of a file with a large header.
+# This is line 1206 of a file with a large header.
+# This is line 1207 of a file with a large header.
+# This is line 1208 of a file with a large header.
+# This is line 1209 of a file with a large header.
+# This is line 1210 of a file with a large header.
+# This is line 1211 of a file with a large header.
+# This is line 1212 of a file with a large header.
+# This is line 1213 of a file with a large header.
+# This is line 1214 of a file with a large header.
+# This is line 1215 of a file with a large header.
+# This is line 1216 of a file with a large header.
+# This is line 1217 of a file with a large header.
+# This is line 1218 of a file with a large header.
+# This is line 1219 of a file with a large header.
+# This is line 1220 of a file with a large header.
+# This is line 1221 of a file with a large header.
+# This is line 1222 of a file with a large header.
+# This is line 1223 of a file with a large header.
+# This is line 1224 of a file with a large header.
+# This is line 1225 of a file with a large header.
+# This is line 1226 of a file with a large header.
+# This is line 1227 of a file with a large header.
+# This is line 1228 of a file with a large header.
+# This is line 1229 of a file with a large header.
+# This is line 1230 of a file with a large header.
+# This is line 1231 of a file with a large header.
+# This is line 1232 of a file with a large header.
+# This is line 1233 of a file with a large header.
+# This is line 1234 of a file with a large header.
+# This is line 1235 of a file with a large header.
+# This is line 1236 of a file with a large header.
+# This is line 1237 of a file with a large header.
+# This is line 1238 of a file with a large header.
+# This is line 1239 of a file with a large header.
+# This is line 1240 of a file with a large header.
+# This is line 1241 of a file with a large header.
+# This is line 1242 of a file with a large header.
+# This is line 1243 of a file with a large header.
+# This is line 1244 of a file with a large header.
+# This is line 1245 of a file with a large header.
+# This is line 1246 of a file with a large header.
+# This is line 1247 of a file with a large header.
+# This is line 1248 of a file with a large header.
+# This is line 1249 of a file with a large header.
+# This is line 1250 of a file with a large header.
+# This is line 1251 of a file with a large header.
+# This is line 1252 of a file with a large header.
+# This is line 1253 of a file with a large header.
+# This is line 1254 of a file with a large header.
+# This is line 1255 of a file with a large header.
+# This is line 1256 of a file with a large header.
+# This is line 1257 of a file with a large header.
+# This is line 1258 of a file with a large header.
+# This is line 1259 of a file with a large header.
+# This is line 1260 of a file with a large header.
+# This is line 1261 of a file with a large header.
+# This is line 1262 of a file with a large header.
+# This is line 1263 of a file with a large header.
+# This is line 1264 of a file with a large header.
+# This is line 1265 of a file with a large header.
+# This is line 1266 of a file with a large header.
+# This is line 1267 of a file with a large header.
+# This is line 1268 of a file with a large header.
+# This is line 1269 of a file with a large header.
+# This is line 1270 of a file with a large header.
+# This is line 1271 of a file with a large header.
+# This is line 1272 of a file with a large header.
+# This is line 1273 of a file with a large header.
+# This is line 1274 of a file with a large header.
+# This is line 1275 of a file with a large header.
+# This is line 1276 of a file with a large header.
+# This is line 1277 of a file with a large header.
+# This is line 1278 of a file with a large header.
+# This is line 1279 of a file with a large header.
+# This is line 1280 of a file with a large header.
+# This is line 1281 of a file with a large header.
+# This is line 1282 of a file with a large header.
+# This is line 1283 of a file with a large header.
+# This is line 1284 of a file with a large header.
+# This is line 1285 of a file with a large header.
+# This is line 1286 of a file with a large header.
+# This is line 1287 of a file with a large header.
+# This is line 1288 of a file with a large header.
+# This is line 1289 of a file with a large header.
+# This is line 1290 of a file with a large header.
+# This is line 1291 of a file with a large header.
+# This is line 1292 of a file with a large header.
+# This is line 1293 of a file with a large header.
+# This is line 1294 of a file with a large header.
+# This is line 1295 of a file with a large header.
+# This is line 1296 of a file with a large header.
+# This is line 1297 of a file with a large header.
+# This is line 1298 of a file with a large header.
+# This is line 1299 of a file with a large header.
+# This is line 1300 of a file with a large header.
+# This is line 1301 of a file with a large header.
+# This is line 1302 of a file with a large header.
+# This is line 1303 of a file with a large header.
+# This is line 1304 of a file with a large header.
+# This is line 1305 of a file with a large header.
+# This is line 1306 of a file with a large header.
+# This is line 1307 of a file with a large header.
+# This is line 1308 of a file with a large header.
+# This is line 1309 of a file with a large header.
+# This is line 1310 of a file with a large header.
+# This is line 1311 of a file with a large header.
+# This is line 1312 of a file with a large header.
+# This is line 1313 of a file with a large header.
+# This is line 1314 of a file with a large header.
+# This is line 1315 of a file with a large header.
+# This is line 1316 of a file with a large header.
+# This is line 1317 of a file with a large header.
+# This is line 1318 of a file with a large header.
+# This is line 1319 of a file with a large header.
+# This is line 1320 of a file with a large header.
+# This is line 1321 of a file with a large header.
+# This is line 1322 of a file with a large header.
+# This is line 1323 of a file with a large header.
+# This is line 1324 of a file with a large header.
+# This is line 1325 of a file with a large header.
+# This is line 1326 of a file with a large header.
+# This is line 1327 of a file with a large header.
+# This is line 1328 of a file with a large header.
+# This is line 1329 of a file with a large header.
+# This is line 1330 of a file with a large header.
+# This is line 1331 of a file with a large header.
+# This is line 1332 of a file with a large header.
+# This is line 1333 of a file with a large header.
+# This is line 1334 of a file with a large header.
+# This is line 1335 of a file with a large header.
+# This is line 1336 of a file with a large header.
+# This is line 1337 of a file with a large header.
+# This is line 1338 of a file with a large header.
+# This is line 1339 of a file with a large header.
+# This is line 1340 of a file with a large header.
+# This is line 1341 of a file with a large header.
+# This is line 1342 of a file with a large header.
+# This is line 1343 of a file with a large header.
+# This is line 1344 of a file with a large header.
+# This is line 1345 of a file with a large header.
+# This is line 1346 of a file with a large header.
+# This is line 1347 of a file with a large header.
+# This is line 1348 of a file with a large header.
+# This is line 1349 of a file with a large header.
+# This is line 1350 of a file with a large header.
+# This is line 1351 of a file with a large header.
+# This is line 1352 of a file with a large header.
+# This is line 1353 of a file with a large header.
+# This is line 1354 of a file with a large header.
+# This is line 1355 of a file with a large header.
+# This is line 1356 of a file with a large header.
+# This is line 1357 of a file with a large header.
+# This is line 1358 of a file with a large header.
+# This is line 1359 of a file with a large header.
+# This is line 1360 of a file with a large header.
+# This is line 1361 of a file with a large header.
+# This is line 1362 of a file with a large header.
+# This is line 1363 of a file with a large header.
+# This is line 1364 of a file with a large header.
+# This is line 1365 of a file with a large header.
+# This is line 1366 of a file with a large header.
+# This is line 1367 of a file with a large header.
+# This is line 1368 of a file with a large header.
+# This is line 1369 of a file with a large header.
+# This is line 1370 of a file with a large header.
+# This is line 1371 of a file with a large header.
+# This is line 1372 of a file with a large header.
+# This is line 1373 of a file with a large header.
+# This is line 1374 of a file with a large header.
+# This is line 1375 of a file with a large header.
+# This is line 1376 of a file with a large header.
+# This is line 1377 of a file with a large header.
+# This is line 1378 of a file with a large header.
+# This is line 1379 of a file with a large header.
+# This is line 1380 of a file with a large header.
+# This is line 1381 of a file with a large header.
+# This is line 1382 of a file with a large header.
+# This is line 1383 of a file with a large header.
+# This is line 1384 of a file with a large header.
+# This is line 1385 of a file with a large header.
+# This is line 1386 of a file with a large header.
+# This is line 1387 of a file with a large header.
+# This is line 1388 of a file with a large header.
+# This is line 1389 of a file with a large header.
+# This is line 1390 of a file with a large header.
+# This is line 1391 of a file with a large header.
+# This is line 1392 of a file with a large header.
+# This is line 1393 of a file with a large header.
+# This is line 1394 of a file with a large header.
+# This is line 1395 of a file with a large header.
+# This is line 1396 of a file with a large header.
+# This is line 1397 of a file with a large header.
+# This is line 1398 of a file with a large header.
+# This is line 1399 of a file with a large header.
+# This is line 1400 of a file with a large header.
+# This is line 1401 of a file with a large header.
+# This is line 1402 of a file with a large header.
+# This is line 1403 of a file with a large header.
+# This is line 1404 of a file with a large header.
+# This is line 1405 of a file with a large header.
+# This is line 1406 of a file with a large header.
+# This is line 1407 of a file with a large header.
+# This is line 1408 of a file with a large header.
+# This is line 1409 of a file with a large header.
+# This is line 1410 of a file with a large header.
+# This is line 1411 of a file with a large header.
+# This is line 1412 of a file with a large header.
+# This is line 1413 of a file with a large header.
+# This is line 1414 of a file with a large header.
+# This is line 1415 of a file with a large header.
+# This is line 1416 of a file with a large header.
+# This is line 1417 of a file with a large header.
+# This is line 1418 of a file with a large header.
+# This is line 1419 of a file with a large header.
+# This is line 1420 of a file with a large header.
+# This is line 1421 of a file with a large header.
+# This is line 1422 of a file with a large header.
+# This is line 1423 of a file with a large header.
+# This is line 1424 of a file with a large header.
+# This is line 1425 of a file with a large header.
+# This is line 1426 of a file with a large header.
+# This is line 1427 of a file with a large header.
+# This is line 1428 of a file with a large header.
+# This is line 1429 of a file with a large header.
+# This is line 1430 of a file with a large header.
+# This is line 1431 of a file with a large header.
+# This is line 1432 of a file with a large header.
+# This is line 1433 of a file with a large header.
+# This is line 1434 of a file with a large header.
+# This is line 1435 of a file with a large header.
+# This is line 1436 of a file with a large header.
+# This is line 1437 of a file with a large header.
+# This is line 1438 of a file with a large header.
+# This is line 1439 of a file with a large header.
+# This is line 1440 of a file with a large header.
+# This is line 1441 of a file with a large header.
+# This is line 1442 of a file with a large header.
+# This is line 1443 of a file with a large header.
+# This is line 1444 of a file with a large header.
+# This is line 1445 of a file with a large header.
+# This is line 1446 of a file with a large header.
+# This is line 1447 of a file with a large header.
+# This is line 1448 of a file with a large header.
+# This is line 1449 of a file with a large header.
+# This is line 1450 of a file with a large header.
+# This is line 1451 of a file with a large header.
+# This is line 1452 of a file with a large header.
+# This is line 1453 of a file with a large header.
+# This is line 1454 of a file with a large header.
+# This is line 1455 of a file with a large header.
+# This is line 1456 of a file with a large header.
+# This is line 1457 of a file with a large header.
+# This is line 1458 of a file with a large header.
+# This is line 1459 of a file with a large header.
+# This is line 1460 of a file with a large header.
+# This is line 1461 of a file with a large header.
+# This is line 1462 of a file with a large header.
+# This is line 1463 of a file with a large header.
+# This is line 1464 of a file with a large header.
+# This is line 1465 of a file with a large header.
+# This is line 1466 of a file with a large header.
+# This is line 1467 of a file with a large header.
+# This is line 1468 of a file with a large header.
+# This is line 1469 of a file with a large header.
+# This is line 1470 of a file with a large header.
+# This is line 1471 of a file with a large header.
+# This is line 1472 of a file with a large header.
+# This is line 1473 of a file with a large header.
+# This is line 1474 of a file with a large header.
+# This is line 1475 of a file with a large header.
+# This is line 1476 of a file with a large header.
+# This is line 1477 of a file with a large header.
+# This is line 1478 of a file with a large header.
+# This is line 1479 of a file with a large header.
+# This is line 1480 of a file with a large header.
+# This is line 1481 of a file with a large header.
+# This is line 1482 of a file with a large header.
+# This is line 1483 of a file with a large header.
+# This is line 1484 of a file with a large header.
+# This is line 1485 of a file with a large header.
+# This is line 1486 of a file with a large header.
+# This is line 1487 of a file with a large header.
+# This is line 1488 of a file with a large header.
+# This is line 1489 of a file with a large header.
+# This is line 1490 of a file with a large header.
+# This is line 1491 of a file with a large header.
+# This is line 1492 of a file with a large header.
+# This is line 1493 of a file with a large header.
+# This is line 1494 of a file with a large header.
+# This is line 1495 of a file with a large header.
+# This is line 1496 of a file with a large header.
+# This is line 1497 of a file with a large header.
+# This is line 1498 of a file with a large header.
+# This is line 1499 of a file with a large header.
+# This is line 1500 of a file with a large header.
+# This is line 1501 of a file with a large header.
+# This is line 1502 of a file with a large header.
+# This is line 1503 of a file with a large header.
+# This is line 1504 of a file with a large header.
+# This is line 1505 of a file with a large header.
+# This is line 1506 of a file with a large header.
+# This is line 1507 of a file with a large header.
+# This is line 1508 of a file with a large header.
+# This is line 1509 of a file with a large header.
+# This is line 1510 of a file with a large header.
+# This is line 1511 of a file with a large header.
+# This is line 1512 of a file with a large header.
+# This is line 1513 of a file with a large header.
+# This is line 1514 of a file with a large header.
+# This is line 1515 of a file with a large header.
+# This is line 1516 of a file with a large header.
+# This is line 1517 of a file with a large header.
+# This is line 1518 of a file with a large header.
+# This is line 1519 of a file with a large header.
+# This is line 1520 of a file with a large header.
+# This is line 1521 of a file with a large header.
+# This is line 1522 of a file with a large header.
+# This is line 1523 of a file with a large header.
+# This is line 1524 of a file with a large header.
+# This is line 1525 of a file with a large header.
+# This is line 1526 of a file with a large header.
+# This is line 1527 of a file with a large header.
+# This is line 1528 of a file with a large header.
+# This is line 1529 of a file with a large header.
+# This is line 1530 of a file with a large header.
+# This is line 1531 of a file with a large header.
+# This is line 1532 of a file with a large header.
+# This is line 1533 of a file with a large header.
+# This is line 1534 of a file with a large header.
+# This is line 1535 of a file with a large header.
+# This is line 1536 of a file with a large header.
+# This is line 1537 of a file with a large header.
+# This is line 1538 of a file with a large header.
+# This is line 1539 of a file with a large header.
+# This is line 1540 of a file with a large header.
+# This is line 1541 of a file with a large header.
+# This is line 1542 of a file with a large header.
+# This is line 1543 of a file with a large header.
+# This is line 1544 of a file with a large header.
+# This is line 1545 of a file with a large header.
+# This is line 1546 of a file with a large header.
+# This is line 1547 of a file with a large header.
+# This is line 1548 of a file with a large header.
+# This is line 1549 of a file with a large header.
+# This is line 1550 of a file with a large header.
+# This is line 1551 of a file with a large header.
+# This is line 1552 of a file with a large header.
+# This is line 1553 of a file with a large header.
+# This is line 1554 of a file with a large header.
+# This is line 1555 of a file with a large header.
+# This is line 1556 of a file with a large header.
+# This is line 1557 of a file with a large header.
+# This is line 1558 of a file with a large header.
+# This is line 1559 of a file with a large header.
+# This is line 1560 of a file with a large header.
+# This is line 1561 of a file with a large header.
+# This is line 1562 of a file with a large header.
+# This is line 1563 of a file with a large header.
+# This is line 1564 of a file with a large header.
+# This is line 1565 of a file with a large header.
+# This is line 1566 of a file with a large header.
+# This is line 1567 of a file with a large header.
+# This is line 1568 of a file with a large header.
+# This is line 1569 of a file with a large header.
+# This is line 1570 of a file with a large header.
+# This is line 1571 of a file with a large header.
+# This is line 1572 of a file with a large header.
+# This is line 1573 of a file with a large header.
+# This is line 1574 of a file with a large header.
+# This is line 1575 of a file with a large header.
+# This is line 1576 of a file with a large header.
+# This is line 1577 of a file with a large header.
+# This is line 1578 of a file with a large header.
+# This is line 1579 of a file with a large header.
+# This is line 1580 of a file with a large header.
+# This is line 1581 of a file with a large header.
+# This is line 1582 of a file with a large header.
+# This is line 1583 of a file with a large header.
+# This is line 1584 of a file with a large header.
+# This is line 1585 of a file with a large header.
+# This is line 1586 of a file with a large header.
+# This is line 1587 of a file with a large header.
+# This is line 1588 of a file with a large header.
+# This is line 1589 of a file with a large header.
+# This is line 1590 of a file with a large header.
+# This is line 1591 of a file with a large header.
+# This is line 1592 of a file with a large header.
+# This is line 1593 of a file with a large header.
+# This is line 1594 of a file with a large header.
+# This is line 1595 of a file with a large header.
+# This is line 1596 of a file with a large header.
+# This is line 1597 of a file with a large header.
+# This is line 1598 of a file with a large header.
+# This is line 1599 of a file with a large header.
+# This is line 1600 of a file with a large header.
+# This is line 1601 of a file with a large header.
+# This is line 1602 of a file with a large header.
+# This is line 1603 of a file with a large header.
+# This is line 1604 of a file with a large header.
+# This is line 1605 of a file with a large header.
+# This is line 1606 of a file with a large header.
+# This is line 1607 of a file with a large header.
+# This is line 1608 of a file with a large header.
+# This is line 1609 of a file with a large header.
+# This is line 1610 of a file with a large header.
+# This is line 1611 of a file with a large header.
+# This is line 1612 of a file with a large header.
+# This is line 1613 of a file with a large header.
+# This is line 1614 of a file with a large header.
+# This is line 1615 of a file with a large header.
+# This is line 1616 of a file with a large header.
+# This is line 1617 of a file with a large header.
+# This is line 1618 of a file with a large header.
+# This is line 1619 of a file with a large header.
+# This is line 1620 of a file with a large header.
+# This is line 1621 of a file with a large header.
+# This is line 1622 of a file with a large header.
+# This is line 1623 of a file with a large header.
+# This is line 1624 of a file with a large header.
+# This is line 1625 of a file with a large header.
+# This is line 1626 of a file with a large header.
+# This is line 1627 of a file with a large header.
+# This is line 1628 of a file with a large header.
+# This is line 1629 of a file with a large header.
+# This is line 1630 of a file with a large header.
+# This is line 1631 of a file with a large header.
+# This is line 1632 of a file with a large header.
+# This is line 1633 of a file with a large header.
+# This is line 1634 of a file with a large header.
+# This is line 1635 of a file with a large header.
+# This is line 1636 of a file with a large header.
+# This is line 1637 of a file with a large header.
+# This is line 1638 of a file with a large header.
+# This is line 1639 of a file with a large header.
+# This is line 1640 of a file with a large header.
+# This is line 1641 of a file with a large header.
+# This is line 1642 of a file with a large header.
+# This is line 1643 of a file with a large header.
+# This is line 1644 of a file with a large header.
+# This is line 1645 of a file with a large header.
+# This is line 1646 of a file with a large header.
+# This is line 1647 of a file with a large header.
+# This is line 1648 of a file with a large header.
+# This is line 1649 of a file with a large header.
+# This is line 1650 of a file with a large header.
+# This is line 1651 of a file with a large header.
+# This is line 1652 of a file with a large header.
+# This is line 1653 of a file with a large header.
+# This is line 1654 of a file with a large header.
+# This is line 1655 of a file with a large header.
+# This is line 1656 of a file with a large header.
+# This is line 1657 of a file with a large header.
+# This is line 1658 of a file with a large header.
+# This is line 1659 of a file with a large header.
+# This is line 1660 of a file with a large header.
+# This is line 1661 of a file with a large header.
+# This is line 1662 of a file with a large header.
+# This is line 1663 of a file with a large header.
+# This is line 1664 of a file with a large header.
+# This is line 1665 of a file with a large header.
+# This is line 1666 of a file with a large header.
+# This is line 1667 of a file with a large header.
+# This is line 1668 of a file with a large header.
+# This is line 1669 of a file with a large header.
+# This is line 1670 of a file with a large header.
+# This is line 1671 of a file with a large header.
+# This is line 1672 of a file with a large header.
+# This is line 1673 of a file with a large header.
+# This is line 1674 of a file with a large header.
+# This is line 1675 of a file with a large header.
+# This is line 1676 of a file with a large header.
+# This is line 1677 of a file with a large header.
+# This is line 1678 of a file with a large header.
+# This is line 1679 of a file with a large header.
+# This is line 1680 of a file with a large header.
+# This is line 1681 of a file with a large header.
+# This is line 1682 of a file with a large header.
+# This is line 1683 of a file with a large header.
+# This is line 1684 of a file with a large header.
+# This is line 1685 of a file with a large header.
+# This is line 1686 of a file with a large header.
+# This is line 1687 of a file with a large header.
+# This is line 1688 of a file with a large header.
+# This is line 1689 of a file with a large header.
+# This is line 1690 of a file with a large header.
+# This is line 1691 of a file with a large header.
+# This is line 1692 of a file with a large header.
+# This is line 1693 of a file with a large header.
+# This is line 1694 of a file with a large header.
+# This is line 1695 of a file with a large header.
+# This is line 1696 of a file with a large header.
+# This is line 1697 of a file with a large header.
+# This is line 1698 of a file with a large header.
+# This is line 1699 of a file with a large header.
+# This is line 1700 of a file with a large header.
+# This is line 1701 of a file with a large header.
+# This is line 1702 of a file with a large header.
+# This is line 1703 of a file with a large header.
+# This is line 1704 of a file with a large header.
+# This is line 1705 of a file with a large header.
+# This is line 1706 of a file with a large header.
+# This is line 1707 of a file with a large header.
+# This is line 1708 of a file with a large header.
+# This is line 1709 of a file with a large header.
+# This is line 1710 of a file with a large header.
+# This is line 1711 of a file with a large header.
+# This is line 1712 of a file with a large header.
+# This is line 1713 of a file with a large header.
+# This is line 1714 of a file with a large header.
+# This is line 1715 of a file with a large header.
+# This is line 1716 of a file with a large header.
+# This is line 1717 of a file with a large header.
+# This is line 1718 of a file with a large header.
+# This is line 1719 of a file with a large header.
+# This is line 1720 of a file with a large header.
+# This is line 1721 of a file with a large header.
+# This is line 1722 of a file with a large header.
+# This is line 1723 of a file with a large header.
+# This is line 1724 of a file with a large header.
+# This is line 1725 of a file with a large header.
+# This is line 1726 of a file with a large header.
+# This is line 1727 of a file with a large header.
+# This is line 1728 of a file with a large header.
+# This is line 1729 of a file with a large header.
+# This is line 1730 of a file with a large header.
+# This is line 1731 of a file with a large header.
+# This is line 1732 of a file with a large header.
+# This is line 1733 of a file with a large header.
+# This is line 1734 of a file with a large header.
+# This is line 1735 of a file with a large header.
+# This is line 1736 of a file with a large header.
+# This is line 1737 of a file with a large header.
+# This is line 1738 of a file with a large header.
+# This is line 1739 of a file with a large header.
+# This is line 1740 of a file with a large header.
+# This is line 1741 of a file with a large header.
+# This is line 1742 of a file with a large header.
+# This is line 1743 of a file with a large header.
+# This is line 1744 of a file with a large header.
+# This is line 1745 of a file with a large header.
+# This is line 1746 of a file with a large header.
+# This is line 1747 of a file with a large header.
+# This is line 1748 of a file with a large header.
+# This is line 1749 of a file with a large header.
+# This is line 1750 of a file with a large header.
+# This is line 1751 of a file with a large header.
+# This is line 1752 of a file with a large header.
+# This is line 1753 of a file with a large header.
+# This is line 1754 of a file with a large header.
+# This is line 1755 of a file with a large header.
+# This is line 1756 of a file with a large header.
+# This is line 1757 of a file with a large header.
+# This is line 1758 of a file with a large header.
+# This is line 1759 of a file with a large header.
+# This is line 1760 of a file with a large header.
+# This is line 1761 of a file with a large header.
+# This is line 1762 of a file with a large header.
+# This is line 1763 of a file with a large header.
+# This is line 1764 of a file with a large header.
+# This is line 1765 of a file with a large header.
+# This is line 1766 of a file with a large header.
+# This is line 1767 of a file with a large header.
+# This is line 1768 of a file with a large header.
+# This is line 1769 of a file with a large header.
+# This is line 1770 of a file with a large header.
+# This is line 1771 of a file with a large header.
+# This is line 1772 of a file with a large header.
+# This is line 1773 of a file with a large header.
+# This is line 1774 of a file with a large header.
+# This is line 1775 of a file with a large header.
+# This is line 1776 of a file with a large header.
+# This is line 1777 of a file with a large header.
+# This is line 1778 of a file with a large header.
+# This is line 1779 of a file with a large header.
+# This is line 1780 of a file with a large header.
+# This is line 1781 of a file with a large header.
+# This is line 1782 of a file with a large header.
+# This is line 1783 of a file with a large header.
+# This is line 1784 of a file with a large header.
+# This is line 1785 of a file with a large header.
+# This is line 1786 of a file with a large header.
+# This is line 1787 of a file with a large header.
+# This is line 1788 of a file with a large header.
+# This is line 1789 of a file with a large header.
+# This is line 1790 of a file with a large header.
+# This is line 1791 of a file with a large header.
+# This is line 1792 of a file with a large header.
+# This is line 1793 of a file with a large header.
+# This is line 1794 of a file with a large header.
+# This is line 1795 of a file with a large header.
+# This is line 1796 of a file with a large header.
+# This is line 1797 of a file with a large header.
+# This is line 1798 of a file with a large header.
+# This is line 1799 of a file with a large header.
+# This is line 1800 of a file with a large header.
+# This is line 1801 of a file with a large header.
+# This is line 1802 of a file with a large header.
+# This is line 1803 of a file with a large header.
+# This is line 1804 of a file with a large header.
+# This is line 1805 of a file with a large header.
+# This is line 1806 of a file with a large header.
+# This is line 1807 of a file with a large header.
+# This is line 1808 of a file with a large header.
+# This is line 1809 of a file with a large header.
+# This is line 1810 of a file with a large header.
+# This is line 1811 of a file with a large header.
+# This is line 1812 of a file with a large header.
+# This is line 1813 of a file with a large header.
+# This is line 1814 of a file with a large header.
+# This is line 1815 of a file with a large header.
+# This is line 1816 of a file with a large header.
+# This is line 1817 of a file with a large header.
+# This is line 1818 of a file with a large header.
+# This is line 1819 of a file with a large header.
+# This is line 1820 of a file with a large header.
+# This is line 1821 of a file with a large header.
+# This is line 1822 of a file with a large header.
+# This is line 1823 of a file with a large header.
+# This is line 1824 of a file with a large header.
+# This is line 1825 of a file with a large header.
+# This is line 1826 of a file with a large header.
+# This is line 1827 of a file with a large header.
+# This is line 1828 of a file with a large header.
+# This is line 1829 of a file with a large header.
+# This is line 1830 of a file with a large header.
+# This is line 1831 of a file with a large header.
+# This is line 1832 of a file with a large header.
+# This is line 1833 of a file with a large header.
+# This is line 1834 of a file with a large header.
+# This is line 1835 of a file with a large header.
+# This is line 1836 of a file with a large header.
+# This is line 1837 of a file with a large header.
+# This is line 1838 of a file with a large header.
+# This is line 1839 of a file with a large header.
+# This is line 1840 of a file with a large header.
+# This is line 1841 of a file with a large header.
+# This is line 1842 of a file with a large header.
+# This is line 1843 of a file with a large header.
+# This is line 1844 of a file with a large header.
+# This is line 1845 of a file with a large header.
+# This is line 1846 of a file with a large header.
+# This is line 1847 of a file with a large header.
+# This is line 1848 of a file with a large header.
+# This is line 1849 of a file with a large header.
+# This is line 1850 of a file with a large header.
+# This is line 1851 of a file with a large header.
+# This is line 1852 of a file with a large header.
+# This is line 1853 of a file with a large header.
+# This is line 1854 of a file with a large header.
+# This is line 1855 of a file with a large header.
+# This is line 1856 of a file with a large header.
+# This is line 1857 of a file with a large header.
+# This is line 1858 of a file with a large header.
+# This is line 1859 of a file with a large header.
+# This is line 1860 of a file with a large header.
+# This is line 1861 of a file with a large header.
+# This is line 1862 of a file with a large header.
+# This is line 1863 of a file with a large header.
+# This is line 1864 of a file with a large header.
+# This is line 1865 of a file with a large header.
+# This is line 1866 of a file with a large header.
+# This is line 1867 of a file with a large header.
+# This is line 1868 of a file with a large header.
+# This is line 1869 of a file with a large header.
+# This is line 1870 of a file with a large header.
+# This is line 1871 of a file with a large header.
+# This is line 1872 of a file with a large header.
+# This is line 1873 of a file with a large header.
+# This is line 1874 of a file with a large header.
+# This is line 1875 of a file with a large header.
+# This is line 1876 of a file with a large header.
+# This is line 1877 of a file with a large header.
+# This is line 1878 of a file with a large header.
+# This is line 1879 of a file with a large header.
+# This is line 1880 of a file with a large header.
+# This is line 1881 of a file with a large header.
+# This is line 1882 of a file with a large header.
+# This is line 1883 of a file with a large header.
+# This is line 1884 of a file with a large header.
+# This is line 1885 of a file with a large header.
+# This is line 1886 of a file with a large header.
+# This is line 1887 of a file with a large header.
+# This is line 1888 of a file with a large header.
+# This is line 1889 of a file with a large header.
+# This is line 1890 of a file with a large header.
+# This is line 1891 of a file with a large header.
+# This is line 1892 of a file with a large header.
+# This is line 1893 of a file with a large header.
+# This is line 1894 of a file with a large header.
+# This is line 1895 of a file with a large header.
+# This is line 1896 of a file with a large header.
+# This is line 1897 of a file with a large header.
+# This is line 1898 of a file with a large header.
+# This is line 1899 of a file with a large header.
+# This is line 1900 of a file with a large header.
+# This is line 1901 of a file with a large header.
+# This is line 1902 of a file with a large header.
+# This is line 1903 of a file with a large header.
+# This is line 1904 of a file with a large header.
+# This is line 1905 of a file with a large header.
+# This is line 1906 of a file with a large header.
+# This is line 1907 of a file with a large header.
+# This is line 1908 of a file with a large header.
+# This is line 1909 of a file with a large header.
+# This is line 1910 of a file with a large header.
+# This is line 1911 of a file with a large header.
+# This is line 1912 of a file with a large header.
+# This is line 1913 of a file with a large header.
+# This is line 1914 of a file with a large header.
+# This is line 1915 of a file with a large header.
+# This is line 1916 of a file with a large header.
+# This is line 1917 of a file with a large header.
+# This is line 1918 of a file with a large header.
+# This is line 1919 of a file with a large header.
+# This is line 1920 of a file with a large header.
+# This is line 1921 of a file with a large header.
+# This is line 1922 of a file with a large header.
+# This is line 1923 of a file with a large header.
+# This is line 1924 of a file with a large header.
+# This is line 1925 of a file with a large header.
+# This is line 1926 of a file with a large header.
+# This is line 1927 of a file with a large header.
+# This is line 1928 of a file with a large header.
+# This is line 1929 of a file with a large header.
+# This is line 1930 of a file with a large header.
+# This is line 1931 of a file with a large header.
+# This is line 1932 of a file with a large header.
+# This is line 1933 of a file with a large header.
+# This is line 1934 of a file with a large header.
+# This is line 1935 of a file with a large header.
+# This is line 1936 of a file with a large header.
+# This is line 1937 of a file with a large header.
+# This is line 1938 of a file with a large header.
+# This is line 1939 of a file with a large header.
+# This is line 1940 of a file with a large header.
+# This is line 1941 of a file with a large header.
+# This is line 1942 of a file with a large header.
+# This is line 1943 of a file with a large header.
+# This is line 1944 of a file with a large header.
+# This is line 1945 of a file with a large header.
+# This is line 1946 of a file with a large header.
+# This is line 1947 of a file with a large header.
+# This is line 1948 of a file with a large header.
+# This is line 1949 of a file with a large header.
+# This is line 1950 of a file with a large header.
+# This is line 1951 of a file with a large header.
+# This is line 1952 of a file with a large header.
+# This is line 1953 of a file with a large header.
+# This is line 1954 of a file with a large header.
+# This is line 1955 of a file with a large header.
+# This is line 1956 of a file with a large header.
+# This is line 1957 of a file with a large header.
+# This is line 1958 of a file with a large header.
+# This is line 1959 of a file with a large header.
+# This is line 1960 of a file with a large header.
+# This is line 1961 of a file with a large header.
+# This is line 1962 of a file with a large header.
+# This is line 1963 of a file with a large header.
+# This is line 1964 of a file with a large header.
+# This is line 1965 of a file with a large header.
+# This is line 1966 of a file with a large header.
+# This is line 1967 of a file with a large header.
+# This is line 1968 of a file with a large header.
+# This is line 1969 of a file with a large header.
+# This is line 1970 of a file with a large header.
+# This is line 1971 of a file with a large header.
+# This is line 1972 of a file with a large header.
+# This is line 1973 of a file with a large header.
+# This is line 1974 of a file with a large header.
+# This is line 1975 of a file with a large header.
+# This is line 1976 of a file with a large header.
+# This is line 1977 of a file with a large header.
+# This is line 1978 of a file with a large header.
+# This is line 1979 of a file with a large header.
+# This is line 1980 of a file with a large header.
+# This is line 1981 of a file with a large header.
+# This is line 1982 of a file with a large header.
+# This is line 1983 of a file with a large header.
+# This is line 1984 of a file with a large header.
+# This is line 1985 of a file with a large header.
+# This is line 1986 of a file with a large header.
+# This is line 1987 of a file with a large header.
+# This is line 1988 of a file with a large header.
+# This is line 1989 of a file with a large header.
+# This is line 1990 of a file with a large header.
+# This is line 1991 of a file with a large header.
+# This is line 1992 of a file with a large header.
+# This is line 1993 of a file with a large header.
+# This is line 1994 of a file with a large header.
+# This is line 1995 of a file with a large header.
+# This is line 1996 of a file with a large header.
+# This is line 1997 of a file with a large header.
+# This is line 1998 of a file with a large header.
+# This is line 1999 of a file with a large header.
+# This is line 2000 of a file with a large header.
+# This is line 2001 of a file with a large header.
+# This is line 2002 of a file with a large header.
+# This is line 2003 of a file with a large header.
+# This is line 2004 of a file with a large header.
+# This is line 2005 of a file with a large header.
+# This is line 2006 of a file with a large header.
+# This is line 2007 of a file with a large header.
+# This is line 2008 of a file with a large header.
+# This is line 2009 of a file with a large header.
+# This is line 2010 of a file with a large header.
+# This is line 2011 of a file with a large header.
+# This is line 2012 of a file with a large header.
+# This is line 2013 of a file with a large header.
+# This is line 2014 of a file with a large header.
+# This is line 2015 of a file with a large header.
+# This is line 2016 of a file with a large header.
+# This is line 2017 of a file with a large header.
+# This is line 2018 of a file with a large header.
+# This is line 2019 of a file with a large header.
+# This is line 2020 of a file with a large header.
+# This is line 2021 of a file with a large header.
+# This is line 2022 of a file with a large header.
+# This is line 2023 of a file with a large header.
+# This is line 2024 of a file with a large header.
+# This is line 2025 of a file with a large header.
+# This is line 2026 of a file with a large header.
+# This is line 2027 of a file with a large header.
+# This is line 2028 of a file with a large header.
+# This is line 2029 of a file with a large header.
+# This is line 2030 of a file with a large header.
+# This is line 2031 of a file with a large header.
+# This is line 2032 of a file with a large header.
+# This is line 2033 of a file with a large header.
+# This is line 2034 of a file with a large header.
+# This is line 2035 of a file with a large header.
+# This is line 2036 of a file with a large header.
+# This is line 2037 of a file with a large header.
+# This is line 2038 of a file with a large header.
+# This is line 2039 of a file with a large header.
+# This is line 2040 of a file with a large header.
+# This is line 2041 of a file with a large header.
+# This is line 2042 of a file with a large header.
+# This is line 2043 of a file with a large header.
+# This is line 2044 of a file with a large header.
+# This is line 2045 of a file with a large header.
+# This is line 2046 of a file with a large header.
+# This is line 2047 of a file with a large header.
+# This is line 2048 of a file with a large header.
+# This is line 2049 of a file with a large header.
+# This is line 2050 of a file with a large header.
+# This is line 2051 of a file with a large header.
+# This is line 2052 of a file with a large header.
+# This is line 2053 of a file with a large header.
+# This is line 2054 of a file with a large header.
+# This is line 2055 of a file with a large header.
+# This is line 2056 of a file with a large header.
+# This is line 2057 of a file with a large header.
+# This is line 2058 of a file with a large header.
+# This is line 2059 of a file with a large header.
+# This is line 2060 of a file with a large header.
+# This is line 2061 of a file with a large header.
+# This is line 2062 of a file with a large header.
+# This is line 2063 of a file with a large header.
+# This is line 2064 of a file with a large header.
+# This is line 2065 of a file with a large header.
+# This is line 2066 of a file with a large header.
+# This is line 2067 of a file with a large header.
+# This is line 2068 of a file with a large header.
+# This is line 2069 of a file with a large header.
+# This is line 2070 of a file with a large header.
+# This is line 2071 of a file with a large header.
+# This is line 2072 of a file with a large header.
+# This is line 2073 of a file with a large header.
+# This is line 2074 of a file with a large header.
+# This is line 2075 of a file with a large header.
+# This is line 2076 of a file with a large header.
+# This is line 2077 of a file with a large header.
+# This is line 2078 of a file with a large header.
+# This is line 2079 of a file with a large header.
+# This is line 2080 of a file with a large header.
+# This is line 2081 of a file with a large header.
+# This is line 2082 of a file with a large header.
+# This is line 2083 of a file with a large header.
+# This is line 2084 of a file with a large header.
+# This is line 2085 of a file with a large header.
+# This is line 2086 of a file with a large header.
+# This is line 2087 of a file with a large header.
+# This is line 2088 of a file with a large header.
+# This is line 2089 of a file with a large header.
+# This is line 2090 of a file with a large header.
+# This is line 2091 of a file with a large header.
+# This is line 2092 of a file with a large header.
+# This is line 2093 of a file with a large header.
+# This is line 2094 of a file with a large header.
+# This is line 2095 of a file with a large header.
+# This is line 2096 of a file with a large header.
+# This is line 2097 of a file with a large header.
+# This is line 2098 of a file with a large header.
+# This is line 2099 of a file with a large header.
+# This is line 2100 of a file with a large header.
+# This is line 2101 of a file with a large header.
+# This is line 2102 of a file with a large header.
+# This is line 2103 of a file with a large header.
+# This is line 2104 of a file with a large header.
+# This is line 2105 of a file with a large header.
+# This is line 2106 of a file with a large header.
+# This is line 2107 of a file with a large header.
+# This is line 2108 of a file with a large header.
+# This is line 2109 of a file with a large header.
+# This is line 2110 of a file with a large header.
+# This is line 2111 of a file with a large header.
+# This is line 2112 of a file with a large header.
+# This is line 2113 of a file with a large header.
+# This is line 2114 of a file with a large header.
+# This is line 2115 of a file with a large header.
+# This is line 2116 of a file with a large header.
+# This is line 2117 of a file with a large header.
+# This is line 2118 of a file with a large header.
+# This is line 2119 of a file with a large header.
+# This is line 2120 of a file with a large header.
+# This is line 2121 of a file with a large header.
+# This is line 2122 of a file with a large header.
+# This is line 2123 of a file with a large header.
+# This is line 2124 of a file with a large header.
+# This is line 2125 of a file with a large header.
+# This is line 2126 of a file with a large header.
+# This is line 2127 of a file with a large header.
+# This is line 2128 of a file with a large header.
+# This is line 2129 of a file with a large header.
+# This is line 2130 of a file with a large header.
+# This is line 2131 of a file with a large header.
+# This is line 2132 of a file with a large header.
+# This is line 2133 of a file with a large header.
+# This is line 2134 of a file with a large header.
+# This is line 2135 of a file with a large header.
+# This is line 2136 of a file with a large header.
+# This is line 2137 of a file with a large header.
+# This is line 2138 of a file with a large header.
+# This is line 2139 of a file with a large header.
+# This is line 2140 of a file with a large header.
+# This is line 2141 of a file with a large header.
+# This is line 2142 of a file with a large header.
+# This is line 2143 of a file with a large header.
+# This is line 2144 of a file with a large header.
+# This is line 2145 of a file with a large header.
+# This is line 2146 of a file with a large header.
+# This is line 2147 of a file with a large header.
+# This is line 2148 of a file with a large header.
+# This is line 2149 of a file with a large header.
+# This is line 2150 of a file with a large header.
+# This is line 2151 of a file with a large header.
+# This is line 2152 of a file with a large header.
+# This is line 2153 of a file with a large header.
+# This is line 2154 of a file with a large header.
+# This is line 2155 of a file with a large header.
+# This is line 2156 of a file with a large header.
+# This is line 2157 of a file with a large header.
+# This is line 2158 of a file with a large header.
+# This is line 2159 of a file with a large header.
+# This is line 2160 of a file with a large header.
+# This is line 2161 of a file with a large header.
+# This is line 2162 of a file with a large header.
+# This is line 2163 of a file with a large header.
+# This is line 2164 of a file with a large header.
+# This is line 2165 of a file with a large header.
+# This is line 2166 of a file with a large header.
+# This is line 2167 of a file with a large header.
+# This is line 2168 of a file with a large header.
+# This is line 2169 of a file with a large header.
+# This is line 2170 of a file with a large header.
+# This is line 2171 of a file with a large header.
+# This is line 2172 of a file with a large header.
+# This is line 2173 of a file with a large header.
+# This is line 2174 of a file with a large header.
+# This is line 2175 of a file with a large header.
+# This is line 2176 of a file with a large header.
+# This is line 2177 of a file with a large header.
+# This is line 2178 of a file with a large header.
+# This is line 2179 of a file with a large header.
+# This is line 2180 of a file with a large header.
+# This is line 2181 of a file with a large header.
+# This is line 2182 of a file with a large header.
+# This is line 2183 of a file with a large header.
+# This is line 2184 of a file with a large header.
+# This is line 2185 of a file with a large header.
+# This is line 2186 of a file with a large header.
+# This is line 2187 of a file with a large header.
+# This is line 2188 of a file with a large header.
+# This is line 2189 of a file with a large header.
+# This is line 2190 of a file with a large header.
+# This is line 2191 of a file with a large header.
+# This is line 2192 of a file with a large header.
+# This is line 2193 of a file with a large header.
+# This is line 2194 of a file with a large header.
+# This is line 2195 of a file with a large header.
+# This is line 2196 of a file with a large header.
+# This is line 2197 of a file with a large header.
+# This is line 2198 of a file with a large header.
+# This is line 2199 of a file with a large header.
+# This is line 2200 of a file with a large header.
+# This is line 2201 of a file with a large header.
+# This is line 2202 of a file with a large header.
+# This is line 2203 of a file with a large header.
+# This is line 2204 of a file with a large header.
+# This is line 2205 of a file with a large header.
+# This is line 2206 of a file with a large header.
+# This is line 2207 of a file with a large header.
+# This is line 2208 of a file with a large header.
+# This is line 2209 of a file with a large header.
+# This is line 2210 of a file with a large header.
+# This is line 2211 of a file with a large header.
+# This is line 2212 of a file with a large header.
+# This is line 2213 of a file with a large header.
+# This is line 2214 of a file with a large header.
+# This is line 2215 of a file with a large header.
+# This is line 2216 of a file with a large header.
+# This is line 2217 of a file with a large header.
+# This is line 2218 of a file with a large header.
+# This is line 2219 of a file with a large header.
+# This is line 2220 of a file with a large header.
+# This is line 2221 of a file with a large header.
+# This is line 2222 of a file with a large header.
+# This is line 2223 of a file with a large header.
+# This is line 2224 of a file with a large header.
+# This is line 2225 of a file with a large header.
+# This is line 2226 of a file with a large header.
+# This is line 2227 of a file with a large header.
+# This is line 2228 of a file with a large header.
+# This is line 2229 of a file with a large header.
+# This is line 2230 of a file with a large header.
+# This is line 2231 of a file with a large header.
+# This is line 2232 of a file with a large header.
+# This is line 2233 of a file with a large header.
+# This is line 2234 of a file with a large header.
+# This is line 2235 of a file with a large header.
+# This is line 2236 of a file with a large header.
+# This is line 2237 of a file with a large header.
+# This is line 2238 of a file with a large header.
+# This is line 2239 of a file with a large header.
+# This is line 2240 of a file with a large header.
+# This is line 2241 of a file with a large header.
+# This is line 2242 of a file with a large header.
+# This is line 2243 of a file with a large header.
+# This is line 2244 of a file with a large header.
+# This is line 2245 of a file with a large header.
+# This is line 2246 of a file with a large header.
+# This is line 2247 of a file with a large header.
+# This is line 2248 of a file with a large header.
+# This is line 2249 of a file with a large header.
+# This is line 2250 of a file with a large header.
+# This is line 2251 of a file with a large header.
+# This is line 2252 of a file with a large header.
+# This is line 2253 of a file with a large header.
+# This is line 2254 of a file with a large header.
+# This is line 2255 of a file with a large header.
+# This is line 2256 of a file with a large header.
+# This is line 2257 of a file with a large header.
+# This is line 2258 of a file with a large header.
+# This is line 2259 of a file with a large header.
+# This is line 2260 of a file with a large header.
+# This is line 2261 of a file with a large header.
+# This is line 2262 of a file with a large header.
+# This is line 2263 of a file with a large header.
+# This is line 2264 of a file with a large header.
+# This is line 2265 of a file with a large header.
+# This is line 2266 of a file with a large header.
+# This is line 2267 of a file with a large header.
+# This is line 2268 of a file with a large header.
+# This is line 2269 of a file with a large header.
+# This is line 2270 of a file with a large header.
+# This is line 2271 of a file with a large header.
+# This is line 2272 of a file with a large header.
+# This is line 2273 of a file with a large header.
+# This is line 2274 of a file with a large header.
+# This is line 2275 of a file with a large header.
+# This is line 2276 of a file with a large header.
+# This is line 2277 of a file with a large header.
+# This is line 2278 of a file with a large header.
+# This is line 2279 of a file with a large header.
+# This is line 2280 of a file with a large header.
+# This is line 2281 of a file with a large header.
+# This is line 2282 of a file with a large header.
+# This is line 2283 of a file with a large header.
+# This is line 2284 of a file with a large header.
+# This is line 2285 of a file with a large header.
+# This is line 2286 of a file with a large header.
+# This is line 2287 of a file with a large header.
+# This is line 2288 of a file with a large header.
+# This is line 2289 of a file with a large header.
+# This is line 2290 of a file with a large header.
+# This is line 2291 of a file with a large header.
+# This is line 2292 of a file with a large header.
+# This is line 2293 of a file with a large header.
+# This is line 2294 of a file with a large header.
+# This is line 2295 of a file with a large header.
+# This is line 2296 of a file with a large header.
+# This is line 2297 of a file with a large header.
+# This is line 2298 of a file with a large header.
+# This is line 2299 of a file with a large header.
+# This is line 2300 of a file with a large header.
+# This is line 2301 of a file with a large header.
+# This is line 2302 of a file with a large header.
+# This is line 2303 of a file with a large header.
+# This is line 2304 of a file with a large header.
+# This is line 2305 of a file with a large header.
+# This is line 2306 of a file with a large header.
+# This is line 2307 of a file with a large header.
+# This is line 2308 of a file with a large header.
+# This is line 2309 of a file with a large header.
+# This is line 2310 of a file with a large header.
+# This is line 2311 of a file with a large header.
+# This is line 2312 of a file with a large header.
+# This is line 2313 of a file with a large header.
+# This is line 2314 of a file with a large header.
+# This is line 2315 of a file with a large header.
+# This is line 2316 of a file with a large header.
+# This is line 2317 of a file with a large header.
+# This is line 2318 of a file with a large header.
+# This is line 2319 of a file with a large header.
+# This is line 2320 of a file with a large header.
+# This is line 2321 of a file with a large header.
+# This is line 2322 of a file with a large header.
+# This is line 2323 of a file with a large header.
+# This is line 2324 of a file with a large header.
+# This is line 2325 of a file with a large header.
+# This is line 2326 of a file with a large header.
+# This is line 2327 of a file with a large header.
+# This is line 2328 of a file with a large header.
+# This is line 2329 of a file with a large header.
+# This is line 2330 of a file with a large header.
+# This is line 2331 of a file with a large header.
+# This is line 2332 of a file with a large header.
+# This is line 2333 of a file with a large header.
+# This is line 2334 of a file with a large header.
+# This is line 2335 of a file with a large header.
+# This is line 2336 of a file with a large header.
+# This is line 2337 of a file with a large header.
+# This is line 2338 of a file with a large header.
+# This is line 2339 of a file with a large header.
+# This is line 2340 of a file with a large header.
+# This is line 2341 of a file with a large header.
+# This is line 2342 of a file with a large header.
+# This is line 2343 of a file with a large header.
+# This is line 2344 of a file with a large header.
+# This is line 2345 of a file with a large header.
+# This is line 2346 of a file with a large header.
+# This is line 2347 of a file with a large header.
+# This is line 2348 of a file with a large header.
+# This is line 2349 of a file with a large header.
+# This is line 2350 of a file with a large header.
+# This is line 2351 of a file with a large header.
+# This is line 2352 of a file with a large header.
+# This is line 2353 of a file with a large header.
+# This is line 2354 of a file with a large header.
+# This is line 2355 of a file with a large header.
+# This is line 2356 of a file with a large header.
+# This is line 2357 of a file with a large header.
+# This is line 2358 of a file with a large header.
+# This is line 2359 of a file with a large header.
+# This is line 2360 of a file with a large header.
+# This is line 2361 of a file with a large header.
+# This is line 2362 of a file with a large header.
+# This is line 2363 of a file with a large header.
+# This is line 2364 of a file with a large header.
+# This is line 2365 of a file with a large header.
+# This is line 2366 of a file with a large header.
+# This is line 2367 of a file with a large header.
+# This is line 2368 of a file with a large header.
+# This is line 2369 of a file with a large header.
+# This is line 2370 of a file with a large header.
+# This is line 2371 of a file with a large header.
+# This is line 2372 of a file with a large header.
+# This is line 2373 of a file with a large header.
+# This is line 2374 of a file with a large header.
+# This is line 2375 of a file with a large header.
+# This is line 2376 of a file with a large header.
+# This is line 2377 of a file with a large header.
+# This is line 2378 of a file with a large header.
+# This is line 2379 of a file with a large header.
+# This is line 2380 of a file with a large header.
+# This is line 2381 of a file with a large header.
+# This is line 2382 of a file with a large header.
+# This is line 2383 of a file with a large header.
+# This is line 2384 of a file with a large header.
+# This is line 2385 of a file with a large header.
+# This is line 2386 of a file with a large header.
+# This is line 2387 of a file with a large header.
+# This is line 2388 of a file with a large header.
+# This is line 2389 of a file with a large header.
+# This is line 2390 of a file with a large header.
+# This is line 2391 of a file with a large header.
+# This is line 2392 of a file with a large header.
+# This is line 2393 of a file with a large header.
+# This is line 2394 of a file with a large header.
+# This is line 2395 of a file with a large header.
+# This is line 2396 of a file with a large header.
+# This is line 2397 of a file with a large header.
+# This is line 2398 of a file with a large header.
+# This is line 2399 of a file with a large header.
+# This is line 2400 of a file with a large header.
+# This is line 2401 of a file with a large header.
+# This is line 2402 of a file with a large header.
+# This is line 2403 of a file with a large header.
+# This is line 2404 of a file with a large header.
+# This is line 2405 of a file with a large header.
+# This is line 2406 of a file with a large header.
+# This is line 2407 of a file with a large header.
+# This is line 2408 of a file with a large header.
+# This is line 2409 of a file with a large header.
+# This is line 2410 of a file with a large header.
+# This is line 2411 of a file with a large header.
+# This is line 2412 of a file with a large header.
+# This is line 2413 of a file with a large header.
+# This is line 2414 of a file with a large header.
+# This is line 2415 of a file with a large header.
+# This is line 2416 of a file with a large header.
+# This is line 2417 of a file with a large header.
+# This is line 2418 of a file with a large header.
+# This is line 2419 of a file with a large header.
+# This is line 2420 of a file with a large header.
+# This is line 2421 of a file with a large header.
+# This is line 2422 of a file with a large header.
+# This is line 2423 of a file with a large header.
+# This is line 2424 of a file with a large header.
+# This is line 2425 of a file with a large header.
+# This is line 2426 of a file with a large header.
+# This is line 2427 of a file with a large header.
+# This is line 2428 of a file with a large header.
+# This is line 2429 of a file with a large header.
+# This is line 2430 of a file with a large header.
+# This is line 2431 of a file with a large header.
+# This is line 2432 of a file with a large header.
+# This is line 2433 of a file with a large header.
+# This is line 2434 of a file with a large header.
+# This is line 2435 of a file with a large header.
+# This is line 2436 of a file with a large header.
+# This is line 2437 of a file with a large header.
+# This is line 2438 of a file with a large header.
+# This is line 2439 of a file with a large header.
+# This is line 2440 of a file with a large header.
+# This is line 2441 of a file with a large header.
+# This is line 2442 of a file with a large header.
+# This is line 2443 of a file with a large header.
+# This is line 2444 of a file with a large header.
+# This is line 2445 of a file with a large header.
+# This is line 2446 of a file with a large header.
+# This is line 2447 of a file with a large header.
+# This is line 2448 of a file with a large header.
+# This is line 2449 of a file with a large header.
+# This is line 2450 of a file with a large header.
+# This is line 2451 of a file with a large header.
+# This is line 2452 of a file with a large header.
+# This is line 2453 of a file with a large header.
+# This is line 2454 of a file with a large header.
+# This is line 2455 of a file with a large header.
+# This is line 2456 of a file with a large header.
+# This is line 2457 of a file with a large header.
+# This is line 2458 of a file with a large header.
+# This is line 2459 of a file with a large header.
+# This is line 2460 of a file with a large header.
+# This is line 2461 of a file with a large header.
+# This is line 2462 of a file with a large header.
+# This is line 2463 of a file with a large header.
+# This is line 2464 of a file with a large header.
+# This is line 2465 of a file with a large header.
+# This is line 2466 of a file with a large header.
+# This is line 2467 of a file with a large header.
+# This is line 2468 of a file with a large header.
+# This is line 2469 of a file with a large header.
+# This is line 2470 of a file with a large header.
+# This is line 2471 of a file with a large header.
+# This is line 2472 of a file with a large header.
+# This is line 2473 of a file with a large header.
+# This is line 2474 of a file with a large header.
+# This is line 2475 of a file with a large header.
+# This is line 2476 of a file with a large header.
+# This is line 2477 of a file with a large header.
+# This is line 2478 of a file with a large header.
+# This is line 2479 of a file with a large header.
+# This is line 2480 of a file with a large header.
+# This is line 2481 of a file with a large header.
+# This is line 2482 of a file with a large header.
+# This is line 2483 of a file with a large header.
+# This is line 2484 of a file with a large header.
+# This is line 2485 of a file with a large header.
+# This is line 2486 of a file with a large header.
+# This is line 2487 of a file with a large header.
+# This is line 2488 of a file with a large header.
+# This is line 2489 of a file with a large header.
+# This is line 2490 of a file with a large header.
+# This is line 2491 of a file with a large header.
+# This is line 2492 of a file with a large header.
+# This is line 2493 of a file with a large header.
+# This is line 2494 of a file with a large header.
+# This is line 2495 of a file with a large header.
+# This is line 2496 of a file with a large header.
+# This is line 2497 of a file with a large header.
+# This is line 2498 of a file with a large header.
+# This is line 2499 of a file with a large header.
+# This is line 2500 of a file with a large header.
+# This is line 2501 of a file with a large header.
+# This is line 2502 of a file with a large header.
+# This is line 2503 of a file with a large header.
+# This is line 2504 of a file with a large header.
+# This is line 2505 of a file with a large header.
+# This is line 2506 of a file with a large header.
+# This is line 2507 of a file with a large header.
+# This is line 2508 of a file with a large header.
+# This is line 2509 of a file with a large header.
+# This is line 2510 of a file with a large header.
+# This is line 2511 of a file with a large header.
+# This is line 2512 of a file with a large header.
+# This is line 2513 of a file with a large header.
+# This is line 2514 of a file with a large header.
+# This is line 2515 of a file with a large header.
+# This is line 2516 of a file with a large header.
+# This is line 2517 of a file with a large header.
+# This is line 2518 of a file with a large header.
+# This is line 2519 of a file with a large header.
+# This is line 2520 of a file with a large header.
+# This is line 2521 of a file with a large header.
+# This is line 2522 of a file with a large header.
+# This is line 2523 of a file with a large header.
+# This is line 2524 of a file with a large header.
+# This is line 2525 of a file with a large header.
+# This is line 2526 of a file with a large header.
+# This is line 2527 of a file with a large header.
+# This is line 2528 of a file with a large header.
+# This is line 2529 of a file with a large header.
+# This is line 2530 of a file with a large header.
+# This is line 2531 of a file with a large header.
+# This is line 2532 of a file with a large header.
+# This is line 2533 of a file with a large header.
+# This is line 2534 of a file with a large header.
+# This is line 2535 of a file with a large header.
+# This is line 2536 of a file with a large header.
+# This is line 2537 of a file with a large header.
+# This is line 2538 of a file with a large header.
+# This is line 2539 of a file with a large header.
+# This is line 2540 of a file with a large header.
+# This is line 2541 of a file with a large header.
+# This is line 2542 of a file with a large header.
+# This is line 2543 of a file with a large header.
+# This is line 2544 of a file with a large header.
+# This is line 2545 of a file with a large header.
+# This is line 2546 of a file with a large header.
+# This is line 2547 of a file with a large header.
+# This is line 2548 of a file with a large header.
+# This is line 2549 of a file with a large header.
+# This is line 2550 of a file with a large header.
+# This is line 2551 of a file with a large header.
+# This is line 2552 of a file with a large header.
+# This is line 2553 of a file with a large header.
+# This is line 2554 of a file with a large header.
+# This is line 2555 of a file with a large header.
+# This is line 2556 of a file with a large header.
+# This is line 2557 of a file with a large header.
+# This is line 2558 of a file with a large header.
+# This is line 2559 of a file with a large header.
+# This is line 2560 of a file with a large header.
+# This is line 2561 of a file with a large header.
+# This is line 2562 of a file with a large header.
+# This is line 2563 of a file with a large header.
+# This is line 2564 of a file with a large header.
+# This is line 2565 of a file with a large header.
+# This is line 2566 of a file with a large header.
+# This is line 2567 of a file with a large header.
+# This is line 2568 of a file with a large header.
+# This is line 2569 of a file with a large header.
+# This is line 2570 of a file with a large header.
+# This is line 2571 of a file with a large header.
+# This is line 2572 of a file with a large header.
+# This is line 2573 of a file with a large header.
+# This is line 2574 of a file with a large header.
+# This is line 2575 of a file with a large header.
+# This is line 2576 of a file with a large header.
+# This is line 2577 of a file with a large header.
+# This is line 2578 of a file with a large header.
+# This is line 2579 of a file with a large header.
+# This is line 2580 of a file with a large header.
+# This is line 2581 of a file with a large header.
+# This is line 2582 of a file with a large header.
+# This is line 2583 of a file with a large header.
+# This is line 2584 of a file with a large header.
+# This is line 2585 of a file with a large header.
+# This is line 2586 of a file with a large header.
+# This is line 2587 of a file with a large header.
+# This is line 2588 of a file with a large header.
+# This is line 2589 of a file with a large header.
+# This is line 2590 of a file with a large header.
+# This is line 2591 of a file with a large header.
+# This is line 2592 of a file with a large header.
+# This is line 2593 of a file with a large header.
+# This is line 2594 of a file with a large header.
+# This is line 2595 of a file with a large header.
+# This is line 2596 of a file with a large header.
+# This is line 2597 of a file with a large header.
+# This is line 2598 of a file with a large header.
+# This is line 2599 of a file with a large header.
+# This is line 2600 of a file with a large header.
+# This is line 2601 of a file with a large header.
+# This is line 2602 of a file with a large header.
+# This is line 2603 of a file with a large header.
+# This is line 2604 of a file with a large header.
+# This is line 2605 of a file with a large header.
+# This is line 2606 of a file with a large header.
+# This is line 2607 of a file with a large header.
+# This is line 2608 of a file with a large header.
+# This is line 2609 of a file with a large header.
+# This is line 2610 of a file with a large header.
+# This is line 2611 of a file with a large header.
+# This is line 2612 of a file with a large header.
+# This is line 2613 of a file with a large header.
+# This is line 2614 of a file with a large header.
+# This is line 2615 of a file with a large header.
+# This is line 2616 of a file with a large header.
+# This is line 2617 of a file with a large header.
+# This is line 2618 of a file with a large header.
+# This is line 2619 of a file with a large header.
+# This is line 2620 of a file with a large header.
+# This is line 2621 of a file with a large header.
+# This is line 2622 of a file with a large header.
+# This is line 2623 of a file with a large header.
+# This is line 2624 of a file with a large header.
+# This is line 2625 of a file with a large header.
+# This is line 2626 of a file with a large header.
+# This is line 2627 of a file with a large header.
+# This is line 2628 of a file with a large header.
+# This is line 2629 of a file with a large header.
+# This is line 2630 of a file with a large header.
+# This is line 2631 of a file with a large header.
+# This is line 2632 of a file with a large header.
+# This is line 2633 of a file with a large header.
+# This is line 2634 of a file with a large header.
+# This is line 2635 of a file with a large header.
+# This is line 2636 of a file with a large header.
+# This is line 2637 of a file with a large header.
+# This is line 2638 of a file with a large header.
+# This is line 2639 of a file with a large header.
+# This is line 2640 of a file with a large header.
+# This is line 2641 of a file with a large header.
+# This is line 2642 of a file with a large header.
+# This is line 2643 of a file with a large header.
+# This is line 2644 of a file with a large header.
+# This is line 2645 of a file with a large header.
+# This is line 2646 of a file with a large header.
+# This is line 2647 of a file with a large header.
+# This is line 2648 of a file with a large header.
+# This is line 2649 of a file with a large header.
+# This is line 2650 of a file with a large header.
+# This is line 2651 of a file with a large header.
+# This is line 2652 of a file with a large header.
+# This is line 2653 of a file with a large header.
+# This is line 2654 of a file with a large header.
+# This is line 2655 of a file with a large header.
+# This is line 2656 of a file with a large header.
+# This is line 2657 of a file with a large header.
+# This is line 2658 of a file with a large header.
+# This is line 2659 of a file with a large header.
+# This is line 2660 of a file with a large header.
+# This is line 2661 of a file with a large header.
+# This is line 2662 of a file with a large header.
+# This is line 2663 of a file with a large header.
+# This is line 2664 of a file with a large header.
+# This is line 2665 of a file with a large header.
+# This is line 2666 of a file with a large header.
+# This is line 2667 of a file with a large header.
+# This is line 2668 of a file with a large header.
+# This is line 2669 of a file with a large header.
+# This is line 2670 of a file with a large header.
+# This is line 2671 of a file with a large header.
+# This is line 2672 of a file with a large header.
+# This is line 2673 of a file with a large header.
+# This is line 2674 of a file with a large header.
+# This is line 2675 of a file with a large header.
+# This is line 2676 of a file with a large header.
+# This is line 2677 of a file with a large header.
+# This is line 2678 of a file with a large header.
+# This is line 2679 of a file with a large header.
+# This is line 2680 of a file with a large header.
+# This is line 2681 of a file with a large header.
+# This is line 2682 of a file with a large header.
+# This is line 2683 of a file with a large header.
+# This is line 2684 of a file with a large header.
+# This is line 2685 of a file with a large header.
+# This is line 2686 of a file with a large header.
+# This is line 2687 of a file with a large header.
+# This is line 2688 of a file with a large header.
+# This is line 2689 of a file with a large header.
+# This is line 2690 of a file with a large header.
+# This is line 2691 of a file with a large header.
+# This is line 2692 of a file with a large header.
+# This is line 2693 of a file with a large header.
+# This is line 2694 of a file with a large header.
+# This is line 2695 of a file with a large header.
+# This is line 2696 of a file with a large header.
+# This is line 2697 of a file with a large header.
+# This is line 2698 of a file with a large header.
+# This is line 2699 of a file with a large header.
+# This is line 2700 of a file with a large header.
+# This is line 2701 of a file with a large header.
+# This is line 2702 of a file with a large header.
+# This is line 2703 of a file with a large header.
+# This is line 2704 of a file with a large header.
+# This is line 2705 of a file with a large header.
+# This is line 2706 of a file with a large header.
+# This is line 2707 of a file with a large header.
+# This is line 2708 of a file with a large header.
+# This is line 2709 of a file with a large header.
+# This is line 2710 of a file with a large header.
+# This is line 2711 of a file with a large header.
+# This is line 2712 of a file with a large header.
+# This is line 2713 of a file with a large header.
+# This is line 2714 of a file with a large header.
+# This is line 2715 of a file with a large header.
+# This is line 2716 of a file with a large header.
+# This is line 2717 of a file with a large header.
+# This is line 2718 of a file with a large header.
+# This is line 2719 of a file with a large header.
+# This is line 2720 of a file with a large header.
+# This is line 2721 of a file with a large header.
+# This is line 2722 of a file with a large header.
+# This is line 2723 of a file with a large header.
+# This is line 2724 of a file with a large header.
+# This is line 2725 of a file with a large header.
+# This is line 2726 of a file with a large header.
+# This is line 2727 of a file with a large header.
+# This is line 2728 of a file with a large header.
+# This is line 2729 of a file with a large header.
+# This is line 2730 of a file with a large header.
+# This is line 2731 of a file with a large header.
+# This is line 2732 of a file with a large header.
+# This is line 2733 of a file with a large header.
+# This is line 2734 of a file with a large header.
+# This is line 2735 of a file with a large header.
+# This is line 2736 of a file with a large header.
+# This is line 2737 of a file with a large header.
+# This is line 2738 of a file with a large header.
+# This is line 2739 of a file with a large header.
+# This is line 2740 of a file with a large header.
+# This is line 2741 of a file with a large header.
+# This is line 2742 of a file with a large header.
+# This is line 2743 of a file with a large header.
+# This is line 2744 of a file with a large header.
+# This is line 2745 of a file with a large header.
+# This is line 2746 of a file with a large header.
+# This is line 2747 of a file with a large header.
+# This is line 2748 of a file with a large header.
+# This is line 2749 of a file with a large header.
+# This is line 2750 of a file with a large header.
+# This is line 2751 of a file with a large header.
+# This is line 2752 of a file with a large header.
+# This is line 2753 of a file with a large header.
+# This is line 2754 of a file with a large header.
+# This is line 2755 of a file with a large header.
+# This is line 2756 of a file with a large header.
+# This is line 2757 of a file with a large header.
+# This is line 2758 of a file with a large header.
+# This is line 2759 of a file with a large header.
+# This is line 2760 of a file with a large header.
+# This is line 2761 of a file with a large header.
+# This is line 2762 of a file with a large header.
+# This is line 2763 of a file with a large header.
+# This is line 2764 of a file with a large header.
+# This is line 2765 of a file with a large header.
+# This is line 2766 of a file with a large header.
+# This is line 2767 of a file with a large header.
+# This is line 2768 of a file with a large header.
+# This is line 2769 of a file with a large header.
+# This is line 2770 of a file with a large header.
+# This is line 2771 of a file with a large header.
+# This is line 2772 of a file with a large header.
+# This is line 2773 of a file with a large header.
+# This is line 2774 of a file with a large header.
+# This is line 2775 of a file with a large header.
+# This is line 2776 of a file with a large header.
+# This is line 2777 of a file with a large header.
+# This is line 2778 of a file with a large header.
+# This is line 2779 of a file with a large header.
+# This is line 2780 of a file with a large header.
+# This is line 2781 of a file with a large header.
+# This is line 2782 of a file with a large header.
+# This is line 2783 of a file with a large header.
+# This is line 2784 of a file with a large header.
+# This is line 2785 of a file with a large header.
+# This is line 2786 of a file with a large header.
+# This is line 2787 of a file with a large header.
+# This is line 2788 of a file with a large header.
+# This is line 2789 of a file with a large header.
+# This is line 2790 of a file with a large header.
+# This is line 2791 of a file with a large header.
+# This is line 2792 of a file with a large header.
+# This is line 2793 of a file with a large header.
+# This is line 2794 of a file with a large header.
+# This is line 2795 of a file with a large header.
+# This is line 2796 of a file with a large header.
+# This is line 2797 of a file with a large header.
+# This is line 2798 of a file with a large header.
+# This is line 2799 of a file with a large header.
+# This is line 2800 of a file with a large header.
+# This is line 2801 of a file with a large header.
+# This is line 2802 of a file with a large header.
+# This is line 2803 of a file with a large header.
+# This is line 2804 of a file with a large header.
+# This is line 2805 of a file with a large header.
+# This is line 2806 of a file with a large header.
+# This is line 2807 of a file with a large header.
+# This is line 2808 of a file with a large header.
+# This is line 2809 of a file with a large header.
+# This is line 2810 of a file with a large header.
+# This is line 2811 of a file with a large header.
+# This is line 2812 of a file with a large header.
+# This is line 2813 of a file with a large header.
+# This is line 2814 of a file with a large header.
+# This is line 2815 of a file with a large header.
+# This is line 2816 of a file with a large header.
+# This is line 2817 of a file with a large header.
+# This is line 2818 of a file with a large header.
+# This is line 2819 of a file with a large header.
+# This is line 2820 of a file with a large header.
+# This is line 2821 of a file with a large header.
+# This is line 2822 of a file with a large header.
+# This is line 2823 of a file with a large header.
+# This is line 2824 of a file with a large header.
+# This is line 2825 of a file with a large header.
+# This is line 2826 of a file with a large header.
+# This is line 2827 of a file with a large header.
+# This is line 2828 of a file with a large header.
+# This is line 2829 of a file with a large header.
+# This is line 2830 of a file with a large header.
+# This is line 2831 of a file with a large header.
+# This is line 2832 of a file with a large header.
+# This is line 2833 of a file with a large header.
+# This is line 2834 of a file with a large header.
+# This is line 2835 of a file with a large header.
+# This is line 2836 of a file with a large header.
+# This is line 2837 of a file with a large header.
+# This is line 2838 of a file with a large header.
+# This is line 2839 of a file with a large header.
+# This is line 2840 of a file with a large header.
+# This is line 2841 of a file with a large header.
+# This is line 2842 of a file with a large header.
+# This is line 2843 of a file with a large header.
+# This is line 2844 of a file with a large header.
+# This is line 2845 of a file with a large header.
+# This is line 2846 of a file with a large header.
+# This is line 2847 of a file with a large header.
+# This is line 2848 of a file with a large header.
+# This is line 2849 of a file with a large header.
+# This is line 2850 of a file with a large header.
+# This is line 2851 of a file with a large header.
+# This is line 2852 of a file with a large header.
+# This is line 2853 of a file with a large header.
+# This is line 2854 of a file with a large header.
+# This is line 2855 of a file with a large header.
+# This is line 2856 of a file with a large header.
+# This is line 2857 of a file with a large header.
+# This is line 2858 of a file with a large header.
+# This is line 2859 of a file with a large header.
+# This is line 2860 of a file with a large header.
+# This is line 2861 of a file with a large header.
+# This is line 2862 of a file with a large header.
+# This is line 2863 of a file with a large header.
+# This is line 2864 of a file with a large header.
+# This is line 2865 of a file with a large header.
+# This is line 2866 of a file with a large header.
+# This is line 2867 of a file with a large header.
+# This is line 2868 of a file with a large header.
+# This is line 2869 of a file with a large header.
+# This is line 2870 of a file with a large header.
+# This is line 2871 of a file with a large header.
+# This is line 2872 of a file with a large header.
+# This is line 2873 of a file with a large header.
+# This is line 2874 of a file with a large header.
+# This is line 2875 of a file with a large header.
+# This is line 2876 of a file with a large header.
+# This is line 2877 of a file with a large header.
+# This is line 2878 of a file with a large header.
+# This is line 2879 of a file with a large header.
+# This is line 2880 of a file with a large header.
+# This is line 2881 of a file with a large header.
+# This is line 2882 of a file with a large header.
+# This is line 2883 of a file with a large header.
+# This is line 2884 of a file with a large header.
+# This is line 2885 of a file with a large header.
+# This is line 2886 of a file with a large header.
+# This is line 2887 of a file with a large header.
+# This is line 2888 of a file with a large header.
+# This is line 2889 of a file with a large header.
+# This is line 2890 of a file with a large header.
+# This is line 2891 of a file with a large header.
+# This is line 2892 of a file with a large header.
+# This is line 2893 of a file with a large header.
+# This is line 2894 of a file with a large header.
+# This is line 2895 of a file with a large header.
+# This is line 2896 of a file with a large header.
+# This is line 2897 of a file with a large header.
+# This is line 2898 of a file with a large header.
+# This is line 2899 of a file with a large header.
+# This is line 2900 of a file with a large header.
+# This is line 2901 of a file with a large header.
+# This is line 2902 of a file with a large header.
+# This is line 2903 of a file with a large header.
+# This is line 2904 of a file with a large header.
+# This is line 2905 of a file with a large header.
+# This is line 2906 of a file with a large header.
+# This is line 2907 of a file with a large header.
+# This is line 2908 of a file with a large header.
+# This is line 2909 of a file with a large header.
+# This is line 2910 of a file with a large header.
+# This is line 2911 of a file with a large header.
+# This is line 2912 of a file with a large header.
+# This is line 2913 of a file with a large header.
+# This is line 2914 of a file with a large header.
+# This is line 2915 of a file with a large header.
+# This is line 2916 of a file with a large header.
+# This is line 2917 of a file with a large header.
+# This is line 2918 of a file with a large header.
+# This is line 2919 of a file with a large header.
+# This is line 2920 of a file with a large header.
+# This is line 2921 of a file with a large header.
+# This is line 2922 of a file with a large header.
+# This is line 2923 of a file with a large header.
+# This is line 2924 of a file with a large header.
+# This is line 2925 of a file with a large header.
+# This is line 2926 of a file with a large header.
+# This is line 2927 of a file with a large header.
+# This is line 2928 of a file with a large header.
+# This is line 2929 of a file with a large header.
+# This is line 2930 of a file with a large header.
+# This is line 2931 of a file with a large header.
+# This is line 2932 of a file with a large header.
+# This is line 2933 of a file with a large header.
+# This is line 2934 of a file with a large header.
+# This is line 2935 of a file with a large header.
+# This is line 2936 of a file with a large header.
+# This is line 2937 of a file with a large header.
+# This is line 2938 of a file with a large header.
+# This is line 2939 of a file with a large header.
+# This is line 2940 of a file with a large header.
+# This is line 2941 of a file with a large header.
+# This is line 2942 of a file with a large header.
+# This is line 2943 of a file with a large header.
+# This is line 2944 of a file with a large header.
+# This is line 2945 of a file with a large header.
+# This is line 2946 of a file with a large header.
+# This is line 2947 of a file with a large header.
+# This is line 2948 of a file with a large header.
+# This is line 2949 of a file with a large header.
+# This is line 2950 of a file with a large header.
+# This is line 2951 of a file with a large header.
+# This is line 2952 of a file with a large header.
+# This is line 2953 of a file with a large header.
+# This is line 2954 of a file with a large header.
+# This is line 2955 of a file with a large header.
+# This is line 2956 of a file with a large header.
+# This is line 2957 of a file with a large header.
+# This is line 2958 of a file with a large header.
+# This is line 2959 of a file with a large header.
+# This is line 2960 of a file with a large header.
+# This is line 2961 of a file with a large header.
+# This is line 2962 of a file with a large header.
+# This is line 2963 of a file with a large header.
+# This is line 2964 of a file with a large header.
+# This is line 2965 of a file with a large header.
+# This is line 2966 of a file with a large header.
+# This is line 2967 of a file with a large header.
+# This is line 2968 of a file with a large header.
+# This is line 2969 of a file with a large header.
+# This is line 2970 of a file with a large header.
+# This is line 2971 of a file with a large header.
+# This is line 2972 of a file with a large header.
+# This is line 2973 of a file with a large header.
+# This is line 2974 of a file with a large header.
+# This is line 2975 of a file with a large header.
+# This is line 2976 of a file with a large header.
+# This is line 2977 of a file with a large header.
+# This is line 2978 of a file with a large header.
+# This is line 2979 of a file with a large header.
+# This is line 2980 of a file with a large header.
+# This is line 2981 of a file with a large header.
+# This is line 2982 of a file with a large header.
+# This is line 2983 of a file with a large header.
+# This is line 2984 of a file with a large header.
+# This is line 2985 of a file with a large header.
+# This is line 2986 of a file with a large header.
+# This is line 2987 of a file with a large header.
+# This is line 2988 of a file with a large header.
+# This is line 2989 of a file with a large header.
+# This is line 2990 of a file with a large header.
+# This is line 2991 of a file with a large header.
+# This is line 2992 of a file with a large header.
+# This is line 2993 of a file with a large header.
+# This is line 2994 of a file with a large header.
+# This is line 2995 of a file with a large header.
+# This is line 2996 of a file with a large header.
+# This is line 2997 of a file with a large header.
+# This is line 2998 of a file with a large header.
+# This is line 2999 of a file with a large header.
+# This is line 3000 of a file with a large header.
+# This is line 3001 of a file with a large header.
+# This is line 3002 of a file with a large header.
+# This is line 3003 of a file with a large header.
+# This is line 3004 of a file with a large header.
+# This is line 3005 of a file with a large header.
+# This is line 3006 of a file with a large header.
+# This is line 3007 of a file with a large header.
+# This is line 3008 of a file with a large header.
+# This is line 3009 of a file with a large header.
+# This is line 3010 of a file with a large header.
+# This is line 3011 of a file with a large header.
+# This is line 3012 of a file with a large header.
+# This is line 3013 of a file with a large header.
+# This is line 3014 of a file with a large header.
+# This is line 3015 of a file with a large header.
+# This is line 3016 of a file with a large header.
+# This is line 3017 of a file with a large header.
+# This is line 3018 of a file with a large header.
+# This is line 3019 of a file with a large header.
+# This is line 3020 of a file with a large header.
+# This is line 3021 of a file with a large header.
+# This is line 3022 of a file with a large header.
+# This is line 3023 of a file with a large header.
+# This is line 3024 of a file with a large header.
+# This is line 3025 of a file with a large header.
+# This is line 3026 of a file with a large header.
+# This is line 3027 of a file with a large header.
+# This is line 3028 of a file with a large header.
+# This is line 3029 of a file with a large header.
+# This is line 3030 of a file with a large header.
+# This is line 3031 of a file with a large header.
+# This is line 3032 of a file with a large header.
+# This is line 3033 of a file with a large header.
+# This is line 3034 of a file with a large header.
+# This is line 3035 of a file with a large header.
+# This is line 3036 of a file with a large header.
+# This is line 3037 of a file with a large header.
+# This is line 3038 of a file with a large header.
+# This is line 3039 of a file with a large header.
+# This is line 3040 of a file with a large header.
+# This is line 3041 of a file with a large header.
+# This is line 3042 of a file with a large header.
+# This is line 3043 of a file with a large header.
+# This is line 3044 of a file with a large header.
+# This is line 3045 of a file with a large header.
+# This is line 3046 of a file with a large header.
+# This is line 3047 of a file with a large header.
+# This is line 3048 of a file with a large header.
+# This is line 3049 of a file with a large header.
+# This is line 3050 of a file with a large header.
+# This is line 3051 of a file with a large header.
+# This is line 3052 of a file with a large header.
+# This is line 3053 of a file with a large header.
+# This is line 3054 of a file with a large header.
+# This is line 3055 of a file with a large header.
+# This is line 3056 of a file with a large header.
+# This is line 3057 of a file with a large header.
+# This is line 3058 of a file with a large header.
+# This is line 3059 of a file with a large header.
+# This is line 3060 of a file with a large header.
+# This is line 3061 of a file with a large header.
+# This is line 3062 of a file with a large header.
+# This is line 3063 of a file with a large header.
+# This is line 3064 of a file with a large header.
+# This is line 3065 of a file with a large header.
+# This is line 3066 of a file with a large header.
+# This is line 3067 of a file with a large header.
+# This is line 3068 of a file with a large header.
+# This is line 3069 of a file with a large header.
+# This is line 3070 of a file with a large header.
+# This is line 3071 of a file with a large header.
+# This is line 3072 of a file with a large header.
+# This is line 3073 of a file with a large header.
+# This is line 3074 of a file with a large header.
+# This is line 3075 of a file with a large header.
+# This is line 3076 of a file with a large header.
+# This is line 3077 of a file with a large header.
+# This is line 3078 of a file with a large header.
+# This is line 3079 of a file with a large header.
+# This is line 3080 of a file with a large header.
+# This is line 3081 of a file with a large header.
+# This is line 3082 of a file with a large header.
+# This is line 3083 of a file with a large header.
+# This is line 3084 of a file with a large header.
+# This is line 3085 of a file with a large header.
+# This is line 3086 of a file with a large header.
+# This is line 3087 of a file with a large header.
+# This is line 3088 of a file with a large header.
+# This is line 3089 of a file with a large header.
+# This is line 3090 of a file with a large header.
+# This is line 3091 of a file with a large header.
+# This is line 3092 of a file with a large header.
+# This is line 3093 of a file with a large header.
+# This is line 3094 of a file with a large header.
+# This is line 3095 of a file with a large header.
+# This is line 3096 of a file with a large header.
+# This is line 3097 of a file with a large header.
+# This is line 3098 of a file with a large header.
+# This is line 3099 of a file with a large header.
+# This is line 3100 of a file with a large header.
+# This is line 3101 of a file with a large header.
+# This is line 3102 of a file with a large header.
+# This is line 3103 of a file with a large header.
+# This is line 3104 of a file with a large header.
+# This is line 3105 of a file with a large header.
+# This is line 3106 of a file with a large header.
+# This is line 3107 of a file with a large header.
+# This is line 3108 of a file with a large header.
+# This is line 3109 of a file with a large header.
+# This is line 3110 of a file with a large header.
+# This is line 3111 of a file with a large header.
+# This is line 3112 of a file with a large header.
+# This is line 3113 of a file with a large header.
+# This is line 3114 of a file with a large header.
+# This is line 3115 of a file with a large header.
+# This is line 3116 of a file with a large header.
+# This is line 3117 of a file with a large header.
+# This is line 3118 of a file with a large header.
+# This is line 3119 of a file with a large header.
+# This is line 3120 of a file with a large header.
+# This is line 3121 of a file with a large header.
+# This is line 3122 of a file with a large header.
+# This is line 3123 of a file with a large header.
+# This is line 3124 of a file with a large header.
+# This is line 3125 of a file with a large header.
+# This is line 3126 of a file with a large header.
+# This is line 3127 of a file with a large header.
+# This is line 3128 of a file with a large header.
+# This is line 3129 of a file with a large header.
+# This is line 3130 of a file with a large header.
+# This is line 3131 of a file with a large header.
+# This is line 3132 of a file with a large header.
+# This is line 3133 of a file with a large header.
+# This is line 3134 of a file with a large header.
+# This is line 3135 of a file with a large header.
+# This is line 3136 of a file with a large header.
+# This is line 3137 of a file with a large header.
+# This is line 3138 of a file with a large header.
+# This is line 3139 of a file with a large header.
+# This is line 3140 of a file with a large header.
+# This is line 3141 of a file with a large header.
+# This is line 3142 of a file with a large header.
+# This is line 3143 of a file with a large header.
+# This is line 3144 of a file with a large header.
+# This is line 3145 of a file with a large header.
+# This is line 3146 of a file with a large header.
+# This is line 3147 of a file with a large header.
+# This is line 3148 of a file with a large header.
+# This is line 3149 of a file with a large header.
+# This is line 3150 of a file with a large header.
+# This is line 3151 of a file with a large header.
+# This is line 3152 of a file with a large header.
+# This is line 3153 of a file with a large header.
+# This is line 3154 of a file with a large header.
+# This is line 3155 of a file with a large header.
+# This is line 3156 of a file with a large header.
+# This is line 3157 of a file with a large header.
+# This is line 3158 of a file with a large header.
+# This is line 3159 of a file with a large header.
+# This is line 3160 of a file with a large header.
+# This is line 3161 of a file with a large header.
+# This is line 3162 of a file with a large header.
+# This is line 3163 of a file with a large header.
+# This is line 3164 of a file with a large header.
+# This is line 3165 of a file with a large header.
+# This is line 3166 of a file with a large header.
+# This is line 3167 of a file with a large header.
+# This is line 3168 of a file with a large header.
+# This is line 3169 of a file with a large header.
+# This is line 3170 of a file with a large header.
+# This is line 3171 of a file with a large header.
+# This is line 3172 of a file with a large header.
+# This is line 3173 of a file with a large header.
+# This is line 3174 of a file with a large header.
+# This is line 3175 of a file with a large header.
+# This is line 3176 of a file with a large header.
+# This is line 3177 of a file with a large header.
+# This is line 3178 of a file with a large header.
+# This is line 3179 of a file with a large header.
+# This is line 3180 of a file with a large header.
+# This is line 3181 of a file with a large header.
+# This is line 3182 of a file with a large header.
+# This is line 3183 of a file with a large header.
+# This is line 3184 of a file with a large header.
+# This is line 3185 of a file with a large header.
+# This is line 3186 of a file with a large header.
+# This is line 3187 of a file with a large header.
+# This is line 3188 of a file with a large header.
+# This is line 3189 of a file with a large header.
+# This is line 3190 of a file with a large header.
+# This is line 3191 of a file with a large header.
+# This is line 3192 of a file with a large header.
+# This is line 3193 of a file with a large header.
+# This is line 3194 of a file with a large header.
+# This is line 3195 of a file with a large header.
+# This is line 3196 of a file with a large header.
+# This is line 3197 of a file with a large header.
+# This is line 3198 of a file with a large header.
+# This is line 3199 of a file with a large header.
+# This is line 3200 of a file with a large header.
+# This is line 3201 of a file with a large header.
+# This is line 3202 of a file with a large header.
+# This is line 3203 of a file with a large header.
+# This is line 3204 of a file with a large header.
+# This is line 3205 of a file with a large header.
+# This is line 3206 of a file with a large header.
+# This is line 3207 of a file with a large header.
+# This is line 3208 of a file with a large header.
+# This is line 3209 of a file with a large header.
+# This is line 3210 of a file with a large header.
+# This is line 3211 of a file with a large header.
+# This is line 3212 of a file with a large header.
+# This is line 3213 of a file with a large header.
+# This is line 3214 of a file with a large header.
+# This is line 3215 of a file with a large header.
+# This is line 3216 of a file with a large header.
+# This is line 3217 of a file with a large header.
+# This is line 3218 of a file with a large header.
+# This is line 3219 of a file with a large header.
+# This is line 3220 of a file with a large header.
+# This is line 3221 of a file with a large header.
+# This is line 3222 of a file with a large header.
+# This is line 3223 of a file with a large header.
+# This is line 3224 of a file with a large header.
+# This is line 3225 of a file with a large header.
+# This is line 3226 of a file with a large header.
+# This is line 3227 of a file with a large header.
+# This is line 3228 of a file with a large header.
+# This is line 3229 of a file with a large header.
+# This is line 3230 of a file with a large header.
+# This is line 3231 of a file with a large header.
+# This is line 3232 of a file with a large header.
+# This is line 3233 of a file with a large header.
+# This is line 3234 of a file with a large header.
+# This is line 3235 of a file with a large header.
+# This is line 3236 of a file with a large header.
+# This is line 3237 of a file with a large header.
+# This is line 3238 of a file with a large header.
+# This is line 3239 of a file with a large header.
+# This is line 3240 of a file with a large header.
+# This is line 3241 of a file with a large header.
+# This is line 3242 of a file with a large header.
+# This is line 3243 of a file with a large header.
+# This is line 3244 of a file with a large header.
+# This is line 3245 of a file with a large header.
+# This is line 3246 of a file with a large header.
+# This is line 3247 of a file with a large header.
+# This is line 3248 of a file with a large header.
+# This is line 3249 of a file with a large header.
+# This is line 3250 of a file with a large header.
+# This is line 3251 of a file with a large header.
+# This is line 3252 of a file with a large header.
+# This is line 3253 of a file with a large header.
+# This is line 3254 of a file with a large header.
+# This is line 3255 of a file with a large header.
+# This is line 3256 of a file with a large header.
+# This is line 3257 of a file with a large header.
+# This is line 3258 of a file with a large header.
+# This is line 3259 of a file with a large header.
+# This is line 3260 of a file with a large header.
+# This is line 3261 of a file with a large header.
+# This is line 3262 of a file with a large header.
+# This is line 3263 of a file with a large header.
+# This is line 3264 of a file with a large header.
+# This is line 3265 of a file with a large header.
+# This is line 3266 of a file with a large header.
+# This is line 3267 of a file with a large header.
+# This is line 3268 of a file with a large header.
+# This is line 3269 of a file with a large header.
+# This is line 3270 of a file with a large header.
+# This is line 3271 of a file with a large header.
+# This is line 3272 of a file with a large header.
+# This is line 3273 of a file with a large header.
+# This is line 3274 of a file with a large header.
+# This is line 3275 of a file with a large header.
+# This is line 3276 of a file with a large header.
+# This is line 3277 of a file with a large header.
+# This is line 3278 of a file with a large header.
+# This is line 3279 of a file with a large header.
+# This is line 3280 of a file with a large header.
+# This is line 3281 of a file with a large header.
+# This is line 3282 of a file with a large header.
+# This is line 3283 of a file with a large header.
+# This is line 3284 of a file with a large header.
+# This is line 3285 of a file with a large header.
+# This is line 3286 of a file with a large header.
+# This is line 3287 of a file with a large header.
+# This is line 3288 of a file with a large header.
+# This is line 3289 of a file with a large header.
+# This is line 3290 of a file with a large header.
+# This is line 3291 of a file with a large header.
+# This is line 3292 of a file with a large header.
+# This is line 3293 of a file with a large header.
+# This is line 3294 of a file with a large header.
+# This is line 3295 of a file with a large header.
+# This is line 3296 of a file with a large header.
+# This is line 3297 of a file with a large header.
+# This is line 3298 of a file with a large header.
+# This is line 3299 of a file with a large header.
+# This is line 3300 of a file with a large header.
+# This is line 3301 of a file with a large header.
+# This is line 3302 of a file with a large header.
+# This is line 3303 of a file with a large header.
+# This is line 3304 of a file with a large header.
+# This is line 3305 of a file with a large header.
+# This is line 3306 of a file with a large header.
+# This is line 3307 of a file with a large header.
+# This is line 3308 of a file with a large header.
+# This is line 3309 of a file with a large header.
+# This is line 3310 of a file with a large header.
+# This is line 3311 of a file with a large header.
+# This is line 3312 of a file with a large header.
+# This is line 3313 of a file with a large header.
+# This is line 3314 of a file with a large header.
+# This is line 3315 of a file with a large header.
+# This is line 3316 of a file with a large header.
+# This is line 3317 of a file with a large header.
+# This is line 3318 of a file with a large header.
+# This is line 3319 of a file with a large header.
+# This is line 3320 of a file with a large header.
+# This is line 3321 of a file with a large header.
+# This is line 3322 of a file with a large header.
+# This is line 3323 of a file with a large header.
+# This is line 3324 of a file with a large header.
+# This is line 3325 of a file with a large header.
+# This is line 3326 of a file with a large header.
+# This is line 3327 of a file with a large header.
+# This is line 3328 of a file with a large header.
+# This is line 3329 of a file with a large header.
+# This is line 3330 of a file with a large header.
+# This is line 3331 of a file with a large header.
+# This is line 3332 of a file with a large header.
+# This is line 3333 of a file with a large header.
+# This is line 3334 of a file with a large header.
+# This is line 3335 of a file with a large header.
+# This is line 3336 of a file with a large header.
+# This is line 3337 of a file with a large header.
+# This is line 3338 of a file with a large header.
+# This is line 3339 of a file with a large header.
+# This is line 3340 of a file with a large header.
+# This is line 3341 of a file with a large header.
+# This is line 3342 of a file with a large header.
+# This is line 3343 of a file with a large header.
+# This is line 3344 of a file with a large header.
+# This is line 3345 of a file with a large header.
+# This is line 3346 of a file with a large header.
+# This is line 3347 of a file with a large header.
+# This is line 3348 of a file with a large header.
+# This is line 3349 of a file with a large header.
+# This is line 3350 of a file with a large header.
+# This is line 3351 of a file with a large header.
+# This is line 3352 of a file with a large header.
+# This is line 3353 of a file with a large header.
+# This is line 3354 of a file with a large header.
+# This is line 3355 of a file with a large header.
+# This is line 3356 of a file with a large header.
+# This is line 3357 of a file with a large header.
+# This is line 3358 of a file with a large header.
+# This is line 3359 of a file with a large header.
+# This is line 3360 of a file with a large header.
+# This is line 3361 of a file with a large header.
+# This is line 3362 of a file with a large header.
+# This is line 3363 of a file with a large header.
+# This is line 3364 of a file with a large header.
+# This is line 3365 of a file with a large header.
+# This is line 3366 of a file with a large header.
+# This is line 3367 of a file with a large header.
+# This is line 3368 of a file with a large header.
+# This is line 3369 of a file with a large header.
+# This is line 3370 of a file with a large header.
+# This is line 3371 of a file with a large header.
+# This is line 3372 of a file with a large header.
+# This is line 3373 of a file with a large header.
+# This is line 3374 of a file with a large header.
+# This is line 3375 of a file with a large header.
+# This is line 3376 of a file with a large header.
+# This is line 3377 of a file with a large header.
+# This is line 3378 of a file with a large header.
+# This is line 3379 of a file with a large header.
+# This is line 3380 of a file with a large header.
+# This is line 3381 of a file with a large header.
+# This is line 3382 of a file with a large header.
+# This is line 3383 of a file with a large header.
+# This is line 3384 of a file with a large header.
+# This is line 3385 of a file with a large header.
+# This is line 3386 of a file with a large header.
+# This is line 3387 of a file with a large header.
+# This is line 3388 of a file with a large header.
+# This is line 3389 of a file with a large header.
+# This is line 3390 of a file with a large header.
+# This is line 3391 of a file with a large header.
+# This is line 3392 of a file with a large header.
+# This is line 3393 of a file with a large header.
+# This is line 3394 of a file with a large header.
+# This is line 3395 of a file with a large header.
+# This is line 3396 of a file with a large header.
+# This is line 3397 of a file with a large header.
+# This is line 3398 of a file with a large header.
+# This is line 3399 of a file with a large header.
+# This is line 3400 of a file with a large header.
+# This is line 3401 of a file with a large header.
+# This is line 3402 of a file with a large header.
+# This is line 3403 of a file with a large header.
+# This is line 3404 of a file with a large header.
+# This is line 3405 of a file with a large header.
+# This is line 3406 of a file with a large header.
+# This is line 3407 of a file with a large header.
+# This is line 3408 of a file with a large header.
+# This is line 3409 of a file with a large header.
+# This is line 3410 of a file with a large header.
+# This is line 3411 of a file with a large header.
+# This is line 3412 of a file with a large header.
+# This is line 3413 of a file with a large header.
+# This is line 3414 of a file with a large header.
+# This is line 3415 of a file with a large header.
+# This is line 3416 of a file with a large header.
+# This is line 3417 of a file with a large header.
+# This is line 3418 of a file with a large header.
+# This is line 3419 of a file with a large header.
+# This is line 3420 of a file with a large header.
+# This is line 3421 of a file with a large header.
+# This is line 3422 of a file with a large header.
+# This is line 3423 of a file with a large header.
+# This is line 3424 of a file with a large header.
+# This is line 3425 of a file with a large header.
+# This is line 3426 of a file with a large header.
+# This is line 3427 of a file with a large header.
+# This is line 3428 of a file with a large header.
+# This is line 3429 of a file with a large header.
+# This is line 3430 of a file with a large header.
+# This is line 3431 of a file with a large header.
+# This is line 3432 of a file with a large header.
+# This is line 3433 of a file with a large header.
+# This is line 3434 of a file with a large header.
+# This is line 3435 of a file with a large header.
+# This is line 3436 of a file with a large header.
+# This is line 3437 of a file with a large header.
+# This is line 3438 of a file with a large header.
+# This is line 3439 of a file with a large header.
+# This is line 3440 of a file with a large header.
+# This is line 3441 of a file with a large header.
+# This is line 3442 of a file with a large header.
+# This is line 3443 of a file with a large header.
+# This is line 3444 of a file with a large header.
+# This is line 3445 of a file with a large header.
+# This is line 3446 of a file with a large header.
+# This is line 3447 of a file with a large header.
+# This is line 3448 of a file with a large header.
+# This is line 3449 of a file with a large header.
+# This is line 3450 of a file with a large header.
+# This is line 3451 of a file with a large header.
+# This is line 3452 of a file with a large header.
+# This is line 3453 of a file with a large header.
+# This is line 3454 of a file with a large header.
+# This is line 3455 of a file with a large header.
+# This is line 3456 of a file with a large header.
+# This is line 3457 of a file with a large header.
+# This is line 3458 of a file with a large header.
+# This is line 3459 of a file with a large header.
+# This is line 3460 of a file with a large header.
+# This is line 3461 of a file with a large header.
+# This is line 3462 of a file with a large header.
+# This is line 3463 of a file with a large header.
+# This is line 3464 of a file with a large header.
+# This is line 3465 of a file with a large header.
+# This is line 3466 of a file with a large header.
+# This is line 3467 of a file with a large header.
+# This is line 3468 of a file with a large header.
+# This is line 3469 of a file with a large header.
+# This is line 3470 of a file with a large header.
+# This is line 3471 of a file with a large header.
+# This is line 3472 of a file with a large header.
+# This is line 3473 of a file with a large header.
+# This is line 3474 of a file with a large header.
+# This is line 3475 of a file with a large header.
+# This is line 3476 of a file with a large header.
+# This is line 3477 of a file with a large header.
+# This is line 3478 of a file with a large header.
+# This is line 3479 of a file with a large header.
+# This is line 3480 of a file with a large header.
+# This is line 3481 of a file with a large header.
+# This is line 3482 of a file with a large header.
+# This is line 3483 of a file with a large header.
+# This is line 3484 of a file with a large header.
+# This is line 3485 of a file with a large header.
+# This is line 3486 of a file with a large header.
+# This is line 3487 of a file with a large header.
+# This is line 3488 of a file with a large header.
+# This is line 3489 of a file with a large header.
+# This is line 3490 of a file with a large header.
+# This is line 3491 of a file with a large header.
+# This is line 3492 of a file with a large header.
+# This is line 3493 of a file with a large header.
+# This is line 3494 of a file with a large header.
+# This is line 3495 of a file with a large header.
+# This is line 3496 of a file with a large header.
+# This is line 3497 of a file with a large header.
+# This is line 3498 of a file with a large header.
+# This is line 3499 of a file with a large header.
+# This is line 3500 of a file with a large header.
+# This is line 3501 of a file with a large header.
+# This is line 3502 of a file with a large header.
+# This is line 3503 of a file with a large header.
+# This is line 3504 of a file with a large header.
+# This is line 3505 of a file with a large header.
+# This is line 3506 of a file with a large header.
+# This is line 3507 of a file with a large header.
+# This is line 3508 of a file with a large header.
+# This is line 3509 of a file with a large header.
+# This is line 3510 of a file with a large header.
+# This is line 3511 of a file with a large header.
+# This is line 3512 of a file with a large header.
+# This is line 3513 of a file with a large header.
+# This is line 3514 of a file with a large header.
+# This is line 3515 of a file with a large header.
+# This is line 3516 of a file with a large header.
+# This is line 3517 of a file with a large header.
+# This is line 3518 of a file with a large header.
+# This is line 3519 of a file with a large header.
+# This is line 3520 of a file with a large header.
+# This is line 3521 of a file with a large header.
+# This is line 3522 of a file with a large header.
+# This is line 3523 of a file with a large header.
+# This is line 3524 of a file with a large header.
+# This is line 3525 of a file with a large header.
+# This is line 3526 of a file with a large header.
+# This is line 3527 of a file with a large header.
+# This is line 3528 of a file with a large header.
+# This is line 3529 of a file with a large header.
+# This is line 3530 of a file with a large header.
+# This is line 3531 of a file with a large header.
+# This is line 3532 of a file with a large header.
+# This is line 3533 of a file with a large header.
+# This is line 3534 of a file with a large header.
+# This is line 3535 of a file with a large header.
+# This is line 3536 of a file with a large header.
+# This is line 3537 of a file with a large header.
+# This is line 3538 of a file with a large header.
+# This is line 3539 of a file with a large header.
+# This is line 3540 of a file with a large header.
+# This is line 3541 of a file with a large header.
+# This is line 3542 of a file with a large header.
+# This is line 3543 of a file with a large header.
+# This is line 3544 of a file with a large header.
+# This is line 3545 of a file with a large header.
+# This is line 3546 of a file with a large header.
+# This is line 3547 of a file with a large header.
+# This is line 3548 of a file with a large header.
+# This is line 3549 of a file with a large header.
+# This is line 3550 of a file with a large header.
+# This is line 3551 of a file with a large header.
+# This is line 3552 of a file with a large header.
+# This is line 3553 of a file with a large header.
+# This is line 3554 of a file with a large header.
+# This is line 3555 of a file with a large header.
+# This is line 3556 of a file with a large header.
+# This is line 3557 of a file with a large header.
+# This is line 3558 of a file with a large header.
+# This is line 3559 of a file with a large header.
+# This is line 3560 of a file with a large header.
+# This is line 3561 of a file with a large header.
+# This is line 3562 of a file with a large header.
+# This is line 3563 of a file with a large header.
+# This is line 3564 of a file with a large header.
+# This is line 3565 of a file with a large header.
+# This is line 3566 of a file with a large header.
+# This is line 3567 of a file with a large header.
+# This is line 3568 of a file with a large header.
+# This is line 3569 of a file with a large header.
+# This is line 3570 of a file with a large header.
+# This is line 3571 of a file with a large header.
+# This is line 3572 of a file with a large header.
+# This is line 3573 of a file with a large header.
+# This is line 3574 of a file with a large header.
+# This is line 3575 of a file with a large header.
+# This is line 3576 of a file with a large header.
+# This is line 3577 of a file with a large header.
+# This is line 3578 of a file with a large header.
+# This is line 3579 of a file with a large header.
+# This is line 3580 of a file with a large header.
+# This is line 3581 of a file with a large header.
+# This is line 3582 of a file with a large header.
+# This is line 3583 of a file with a large header.
+# This is line 3584 of a file with a large header.
+# This is line 3585 of a file with a large header.
+# This is line 3586 of a file with a large header.
+# This is line 3587 of a file with a large header.
+# This is line 3588 of a file with a large header.
+# This is line 3589 of a file with a large header.
+# This is line 3590 of a file with a large header.
+# This is line 3591 of a file with a large header.
+# This is line 3592 of a file with a large header.
+# This is line 3593 of a file with a large header.
+# This is line 3594 of a file with a large header.
+# This is line 3595 of a file with a large header.
+# This is line 3596 of a file with a large header.
+# This is line 3597 of a file with a large header.
+# This is line 3598 of a file with a large header.
+# This is line 3599 of a file with a large header.
+# This is line 3600 of a file with a large header.
+# This is line 3601 of a file with a large header.
+# This is line 3602 of a file with a large header.
+# This is line 3603 of a file with a large header.
+# This is line 3604 of a file with a large header.
+# This is line 3605 of a file with a large header.
+# This is line 3606 of a file with a large header.
+# This is line 3607 of a file with a large header.
+# This is line 3608 of a file with a large header.
+# This is line 3609 of a file with a large header.
+# This is line 3610 of a file with a large header.
+# This is line 3611 of a file with a large header.
+# This is line 3612 of a file with a large header.
+# This is line 3613 of a file with a large header.
+# This is line 3614 of a file with a large header.
+# This is line 3615 of a file with a large header.
+# This is line 3616 of a file with a large header.
+# This is line 3617 of a file with a large header.
+# This is line 3618 of a file with a large header.
+# This is line 3619 of a file with a large header.
+# This is line 3620 of a file with a large header.
+# This is line 3621 of a file with a large header.
+# This is line 3622 of a file with a large header.
+# This is line 3623 of a file with a large header.
+# This is line 3624 of a file with a large header.
+# This is line 3625 of a file with a large header.
+# This is line 3626 of a file with a large header.
+# This is line 3627 of a file with a large header.
+# This is line 3628 of a file with a large header.
+# This is line 3629 of a file with a large header.
+# This is line 3630 of a file with a large header.
+# This is line 3631 of a file with a large header.
+# This is line 3632 of a file with a large header.
+# This is line 3633 of a file with a large header.
+# This is line 3634 of a file with a large header.
+# This is line 3635 of a file with a large header.
+# This is line 3636 of a file with a large header.
+# This is line 3637 of a file with a large header.
+# This is line 3638 of a file with a large header.
+# This is line 3639 of a file with a large header.
+# This is line 3640 of a file with a large header.
+# This is line 3641 of a file with a large header.
+# This is line 3642 of a file with a large header.
+# This is line 3643 of a file with a large header.
+# This is line 3644 of a file with a large header.
+# This is line 3645 of a file with a large header.
+# This is line 3646 of a file with a large header.
+# This is line 3647 of a file with a large header.
+# This is line 3648 of a file with a large header.
+# This is line 3649 of a file with a large header.
+# This is line 3650 of a file with a large header.
+# This is line 3651 of a file with a large header.
+# This is line 3652 of a file with a large header.
+# This is line 3653 of a file with a large header.
+# This is line 3654 of a file with a large header.
+# This is line 3655 of a file with a large header.
+# This is line 3656 of a file with a large header.
+# This is line 3657 of a file with a large header.
+# This is line 3658 of a file with a large header.
+# This is line 3659 of a file with a large header.
+# This is line 3660 of a file with a large header.
+# This is line 3661 of a file with a large header.
+# This is line 3662 of a file with a large header.
+# This is line 3663 of a file with a large header.
+# This is line 3664 of a file with a large header.
+# This is line 3665 of a file with a large header.
+# This is line 3666 of a file with a large header.
+# This is line 3667 of a file with a large header.
+# This is line 3668 of a file with a large header.
+# This is line 3669 of a file with a large header.
+# This is line 3670 of a file with a large header.
+# This is line 3671 of a file with a large header.
+# This is line 3672 of a file with a large header.
+# This is line 3673 of a file with a large header.
+# This is line 3674 of a file with a large header.
+# This is line 3675 of a file with a large header.
+# This is line 3676 of a file with a large header.
+# This is line 3677 of a file with a large header.
+# This is line 3678 of a file with a large header.
+# This is line 3679 of a file with a large header.
+# This is line 3680 of a file with a large header.
+# This is line 3681 of a file with a large header.
+# This is line 3682 of a file with a large header.
+# This is line 3683 of a file with a large header.
+# This is line 3684 of a file with a large header.
+# This is line 3685 of a file with a large header.
+# This is line 3686 of a file with a large header.
+# This is line 3687 of a file with a large header.
+# This is line 3688 of a file with a large header.
+# This is line 3689 of a file with a large header.
+# This is line 3690 of a file with a large header.
+# This is line 3691 of a file with a large header.
+# This is line 3692 of a file with a large header.
+# This is line 3693 of a file with a large header.
+# This is line 3694 of a file with a large header.
+# This is line 3695 of a file with a large header.
+# This is line 3696 of a file with a large header.
+# This is line 3697 of a file with a large header.
+# This is line 3698 of a file with a large header.
+# This is line 3699 of a file with a large header.
+# This is line 3700 of a file with a large header.
+# This is line 3701 of a file with a large header.
+# This is line 3702 of a file with a large header.
+# This is line 3703 of a file with a large header.
+# This is line 3704 of a file with a large header.
+# This is line 3705 of a file with a large header.
+# This is line 3706 of a file with a large header.
+# This is line 3707 of a file with a large header.
+# This is line 3708 of a file with a large header.
+# This is line 3709 of a file with a large header.
+# This is line 3710 of a file with a large header.
+# This is line 3711 of a file with a large header.
+# This is line 3712 of a file with a large header.
+# This is line 3713 of a file with a large header.
+# This is line 3714 of a file with a large header.
+# This is line 3715 of a file with a large header.
+# This is line 3716 of a file with a large header.
+# This is line 3717 of a file with a large header.
+# This is line 3718 of a file with a large header.
+# This is line 3719 of a file with a large header.
+# This is line 3720 of a file with a large header.
+# This is line 3721 of a file with a large header.
+# This is line 3722 of a file with a large header.
+# This is line 3723 of a file with a large header.
+# This is line 3724 of a file with a large header.
+# This is line 3725 of a file with a large header.
+# This is line 3726 of a file with a large header.
+# This is line 3727 of a file with a large header.
+# This is line 3728 of a file with a large header.
+# This is line 3729 of a file with a large header.
+# This is line 3730 of a file with a large header.
+# This is line 3731 of a file with a large header.
+# This is line 3732 of a file with a large header.
+# This is line 3733 of a file with a large header.
+# This is line 3734 of a file with a large header.
+# This is line 3735 of a file with a large header.
+# This is line 3736 of a file with a large header.
+# This is line 3737 of a file with a large header.
+# This is line 3738 of a file with a large header.
+# This is line 3739 of a file with a large header.
+# This is line 3740 of a file with a large header.
+# This is line 3741 of a file with a large header.
+# This is line 3742 of a file with a large header.
+# This is line 3743 of a file with a large header.
+# This is line 3744 of a file with a large header.
+# This is line 3745 of a file with a large header.
+# This is line 3746 of a file with a large header.
+# This is line 3747 of a file with a large header.
+# This is line 3748 of a file with a large header.
+# This is line 3749 of a file with a large header.
+# This is line 3750 of a file with a large header.
+# This is line 3751 of a file with a large header.
+# This is line 3752 of a file with a large header.
+# This is line 3753 of a file with a large header.
+# This is line 3754 of a file with a large header.
+# This is line 3755 of a file with a large header.
+# This is line 3756 of a file with a large header.
+# This is line 3757 of a file with a large header.
+# This is line 3758 of a file with a large header.
+# This is line 3759 of a file with a large header.
+# This is line 3760 of a file with a large header.
+# This is line 3761 of a file with a large header.
+# This is line 3762 of a file with a large header.
+# This is line 3763 of a file with a large header.
+# This is line 3764 of a file with a large header.
+# This is line 3765 of a file with a large header.
+# This is line 3766 of a file with a large header.
+# This is line 3767 of a file with a large header.
+# This is line 3768 of a file with a large header.
+# This is line 3769 of a file with a large header.
+# This is line 3770 of a file with a large header.
+# This is line 3771 of a file with a large header.
+# This is line 3772 of a file with a large header.
+# This is line 3773 of a file with a large header.
+# This is line 3774 of a file with a large header.
+# This is line 3775 of a file with a large header.
+# This is line 3776 of a file with a large header.
+# This is line 3777 of a file with a large header.
+# This is line 3778 of a file with a large header.
+# This is line 3779 of a file with a large header.
+# This is line 3780 of a file with a large header.
+# This is line 3781 of a file with a large header.
+# This is line 3782 of a file with a large header.
+# This is line 3783 of a file with a large header.
+# This is line 3784 of a file with a large header.
+# This is line 3785 of a file with a large header.
+# This is line 3786 of a file with a large header.
+# This is line 3787 of a file with a large header.
+# This is line 3788 of a file with a large header.
+# This is line 3789 of a file with a large header.
+# This is line 3790 of a file with a large header.
+# This is line 3791 of a file with a large header.
+# This is line 3792 of a file with a large header.
+# This is line 3793 of a file with a large header.
+# This is line 3794 of a file with a large header.
+# This is line 3795 of a file with a large header.
+# This is line 3796 of a file with a large header.
+# This is line 3797 of a file with a large header.
+# This is line 3798 of a file with a large header.
+# This is line 3799 of a file with a large header.
+# This is line 3800 of a file with a large header.
+# This is line 3801 of a file with a large header.
+# This is line 3802 of a file with a large header.
+# This is line 3803 of a file with a large header.
+# This is line 3804 of a file with a large header.
+# This is line 3805 of a file with a large header.
+# This is line 3806 of a file with a large header.
+# This is line 3807 of a file with a large header.
+# This is line 3808 of a file with a large header.
+# This is line 3809 of a file with a large header.
+# This is line 3810 of a file with a large header.
+# This is line 3811 of a file with a large header.
+# This is line 3812 of a file with a large header.
+# This is line 3813 of a file with a large header.
+# This is line 3814 of a file with a large header.
+# This is line 3815 of a file with a large header.
+# This is line 3816 of a file with a large header.
+# This is line 3817 of a file with a large header.
+# This is line 3818 of a file with a large header.
+# This is line 3819 of a file with a large header.
+# This is line 3820 of a file with a large header.
+# This is line 3821 of a file with a large header.
+# This is line 3822 of a file with a large header.
+# This is line 3823 of a file with a large header.
+# This is line 3824 of a file with a large header.
+# This is line 3825 of a file with a large header.
+# This is line 3826 of a file with a large header.
+# This is line 3827 of a file with a large header.
+# This is line 3828 of a file with a large header.
+# This is line 3829 of a file with a large header.
+# This is line 3830 of a file with a large header.
+# This is line 3831 of a file with a large header.
+# This is line 3832 of a file with a large header.
+# This is line 3833 of a file with a large header.
+# This is line 3834 of a file with a large header.
+# This is line 3835 of a file with a large header.
+# This is line 3836 of a file with a large header.
+# This is line 3837 of a file with a large header.
+# This is line 3838 of a file with a large header.
+# This is line 3839 of a file with a large header.
+# This is line 3840 of a file with a large header.
+# This is line 3841 of a file with a large header.
+# This is line 3842 of a file with a large header.
+# This is line 3843 of a file with a large header.
+# This is line 3844 of a file with a large header.
+# This is line 3845 of a file with a large header.
+# This is line 3846 of a file with a large header.
+# This is line 3847 of a file with a large header.
+# This is line 3848 of a file with a large header.
+# This is line 3849 of a file with a large header.
+# This is line 3850 of a file with a large header.
+# This is line 3851 of a file with a large header.
+# This is line 3852 of a file with a large header.
+# This is line 3853 of a file with a large header.
+# This is line 3854 of a file with a large header.
+# This is line 3855 of a file with a large header.
+# This is line 3856 of a file with a large header.
+# This is line 3857 of a file with a large header.
+# This is line 3858 of a file with a large header.
+# This is line 3859 of a file with a large header.
+# This is line 3860 of a file with a large header.
+# This is line 3861 of a file with a large header.
+# This is line 3862 of a file with a large header.
+# This is line 3863 of a file with a large header.
+# This is line 3864 of a file with a large header.
+# This is line 3865 of a file with a large header.
+# This is line 3866 of a file with a large header.
+# This is line 3867 of a file with a large header.
+# This is line 3868 of a file with a large header.
+# This is line 3869 of a file with a large header.
+# This is line 3870 of a file with a large header.
+# This is line 3871 of a file with a large header.
+# This is line 3872 of a file with a large header.
+# This is line 3873 of a file with a large header.
+# This is line 3874 of a file with a large header.
+# This is line 3875 of a file with a large header.
+# This is line 3876 of a file with a large header.
+# This is line 3877 of a file with a large header.
+# This is line 3878 of a file with a large header.
+# This is line 3879 of a file with a large header.
+# This is line 3880 of a file with a large header.
+# This is line 3881 of a file with a large header.
+# This is line 3882 of a file with a large header.
+# This is line 3883 of a file with a large header.
+# This is line 3884 of a file with a large header.
+# This is line 3885 of a file with a large header.
+# This is line 3886 of a file with a large header.
+# This is line 3887 of a file with a large header.
+# This is line 3888 of a file with a large header.
+# This is line 3889 of a file with a large header.
+# This is line 3890 of a file with a large header.
+# This is line 3891 of a file with a large header.
+# This is line 3892 of a file with a large header.
+# This is line 3893 of a file with a large header.
+# This is line 3894 of a file with a large header.
+# This is line 3895 of a file with a large header.
+# This is line 3896 of a file with a large header.
+# This is line 3897 of a file with a large header.
+# This is line 3898 of a file with a large header.
+# This is line 3899 of a file with a large header.
+# This is line 3900 of a file with a large header.
+# This is line 3901 of a file with a large header.
+# This is line 3902 of a file with a large header.
+# This is line 3903 of a file with a large header.
+# This is line 3904 of a file with a large header.
+# This is line 3905 of a file with a large header.
+# This is line 3906 of a file with a large header.
+# This is line 3907 of a file with a large header.
+# This is line 3908 of a file with a large header.
+# This is line 3909 of a file with a large header.
+# This is line 3910 of a file with a large header.
+# This is line 3911 of a file with a large header.
+# This is line 3912 of a file with a large header.
+# This is line 3913 of a file with a large header.
+# This is line 3914 of a file with a large header.
+# This is line 3915 of a file with a large header.
+# This is line 3916 of a file with a large header.
+# This is line 3917 of a file with a large header.
+# This is line 3918 of a file with a large header.
+# This is line 3919 of a file with a large header.
+# This is line 3920 of a file with a large header.
+# This is line 3921 of a file with a large header.
+# This is line 3922 of a file with a large header.
+# This is line 3923 of a file with a large header.
+# This is line 3924 of a file with a large header.
+# This is line 3925 of a file with a large header.
+# This is line 3926 of a file with a large header.
+# This is line 3927 of a file with a large header.
+# This is line 3928 of a file with a large header.
+# This is line 3929 of a file with a large header.
+# This is line 3930 of a file with a large header.
+# This is line 3931 of a file with a large header.
+# This is line 3932 of a file with a large header.
+# This is line 3933 of a file with a large header.
+# This is line 3934 of a file with a large header.
+# This is line 3935 of a file with a large header.
+# This is line 3936 of a file with a large header.
+# This is line 3937 of a file with a large header.
+# This is line 3938 of a file with a large header.
+# This is line 3939 of a file with a large header.
+# This is line 3940 of a file with a large header.
+# This is line 3941 of a file with a large header.
+# This is line 3942 of a file with a large header.
+# This is line 3943 of a file with a large header.
+# This is line 3944 of a file with a large header.
+# This is line 3945 of a file with a large header.
+# This is line 3946 of a file with a large header.
+# This is line 3947 of a file with a large header.
+# This is line 3948 of a file with a large header.
+# This is line 3949 of a file with a large header.
+# This is line 3950 of a file with a large header.
+# This is line 3951 of a file with a large header.
+# This is line 3952 of a file with a large header.
+# This is line 3953 of a file with a large header.
+# This is line 3954 of a file with a large header.
+# This is line 3955 of a file with a large header.
+# This is line 3956 of a file with a large header.
+# This is line 3957 of a file with a large header.
+# This is line 3958 of a file with a large header.
+# This is line 3959 of a file with a large header.
+# This is line 3960 of a file with a large header.
+# This is line 3961 of a file with a large header.
+# This is line 3962 of a file with a large header.
+# This is line 3963 of a file with a large header.
+# This is line 3964 of a file with a large header.
+# This is line 3965 of a file with a large header.
+# This is line 3966 of a file with a large header.
+# This is line 3967 of a file with a large header.
+# This is line 3968 of a file with a large header.
+# This is line 3969 of a file with a large header.
+# This is line 3970 of a file with a large header.
+# This is line 3971 of a file with a large header.
+# This is line 3972 of a file with a large header.
+# This is line 3973 of a file with a large header.
+# This is line 3974 of a file with a large header.
+# This is line 3975 of a file with a large header.
+# This is line 3976 of a file with a large header.
+# This is line 3977 of a file with a large header.
+# This is line 3978 of a file with a large header.
+# This is line 3979 of a file with a large header.
+# This is line 3980 of a file with a large header.
+# This is line 3981 of a file with a large header.
+# This is line 3982 of a file with a large header.
+# This is line 3983 of a file with a large header.
+# This is line 3984 of a file with a large header.
+# This is line 3985 of a file with a large header.
+# This is line 3986 of a file with a large header.
+# This is line 3987 of a file with a large header.
+# This is line 3988 of a file with a large header.
+# This is line 3989 of a file with a large header.
+# This is line 3990 of a file with a large header.
+# This is line 3991 of a file with a large header.
+# This is line 3992 of a file with a large header.
+# This is line 3993 of a file with a large header.
+# This is line 3994 of a file with a large header.
+# This is line 3995 of a file with a large header.
+# This is line 3996 of a file with a large header.
+# This is line 3997 of a file with a large header.
+# This is line 3998 of a file with a large header.
+# This is line 3999 of a file with a large header.
+chr1 10 20 a1 1 +
+chr1 100 200 a2 2 -
diff --git a/test/intersect/a_withLargeHeader_bgzipped.bed.gz b/test/intersect/a_withLargeHeader_bgzipped.bed.gz
new file mode 100644
index 0000000..e5e87f3
Binary files /dev/null and b/test/intersect/a_withLargeHeader_bgzipped.bed.gz differ
diff --git a/test/intersect/a_withLargeHeader_gzipped.bed.gz b/test/intersect/a_withLargeHeader_gzipped.bed.gz
new file mode 100644
index 0000000..54acb81
Binary files /dev/null and b/test/intersect/a_withLargeHeader_gzipped.bed.gz differ
diff --git a/test/intersect/a_with_bothUnmapped.bam b/test/intersect/a_with_bothUnmapped.bam
new file mode 100644
index 0000000..c8959e5
Binary files /dev/null and b/test/intersect/a_with_bothUnmapped.bam differ
diff --git a/test/intersect/bed3.bed b/test/intersect/bed3.bed
new file mode 100644
index 0000000..d6c80bc
--- /dev/null
+++ b/test/intersect/bed3.bed
@@ -0,0 +1 @@
+chr1 10 20
diff --git a/test/intersect/bed4.bed b/test/intersect/bed4.bed
new file mode 100644
index 0000000..d7d2287
--- /dev/null
+++ b/test/intersect/bed4.bed
@@ -0,0 +1 @@
+chr1 10 20 345.7
diff --git a/test/intersect/bed5.bed b/test/intersect/bed5.bed
new file mode 100644
index 0000000..614b752
--- /dev/null
+++ b/test/intersect/bed5.bed
@@ -0,0 +1 @@
+chr1 10 20 345.7 why?
diff --git a/test/intersect/bed6.bed b/test/intersect/bed6.bed
new file mode 100644
index 0000000..8382fe1
--- /dev/null
+++ b/test/intersect/bed6.bed
@@ -0,0 +1 @@
+chr1 10 20 345.7 why? 11
diff --git a/test/intersect/bed6.strand.bed b/test/intersect/bed6.strand.bed
new file mode 100644
index 0000000..6c6e21e
--- /dev/null
+++ b/test/intersect/bed6.strand.bed
@@ -0,0 +1 @@
+chr1 10 20 345.7 why? -
diff --git a/test/intersect/bed6.strand2.bed b/test/intersect/bed6.strand2.bed
new file mode 100644
index 0000000..e5d0d25
--- /dev/null
+++ b/test/intersect/bed6.strand2.bed
@@ -0,0 +1,2 @@
+chr1 10 20 345.7 why? -
+chr1 11 21 345.7 why? +
diff --git a/test/intersect/bedplus.bed b/test/intersect/bedplus.bed
new file mode 100644
index 0000000..f2d6984
--- /dev/null
+++ b/test/intersect/bedplus.bed
@@ -0,0 +1 @@
+chr1 10 20 345.7 why? 11 foo bar biz 11 bang bop 99
diff --git a/test/intersect/chromOrderA.bed b/test/intersect/chromOrderA.bed
new file mode 100644
index 0000000..6937acf
--- /dev/null
+++ b/test/intersect/chromOrderA.bed
@@ -0,0 +1,6 @@
+chr1 10 20 a1 100 +
+chr2 10 20 a2 100 +
+chr10 10 20 a3 100 +
+chr11 10 20 a4 100 +
+chrX 10 20 a5 100 +
+chrM 10 20 a6 100 +
diff --git a/test/intersect/chromOrderB.bed b/test/intersect/chromOrderB.bed
new file mode 100644
index 0000000..2f2cad1
--- /dev/null
+++ b/test/intersect/chromOrderB.bed
@@ -0,0 +1,12 @@
+chr1 15 25 a1 100 +
+chr1 30 40 a1 100 +
+chr2 15 25 a2 100 +
+chr2 30 40 a1 100 +
+chr10 15 25 a3 100 +
+chr10 30 40 a1 100 +
+chr11 15 25 a4 100 +
+chr11 30 40 a1 100 +
+chrX 15 25 a5 100 +
+chrX 30 40 a1 100 +
+chrM 15 25 a6 100 +
+chrM 30 40 a1 100 +
diff --git a/test/intersect/chromsOutOfOrder.bed b/test/intersect/chromsOutOfOrder.bed
new file mode 100644
index 0000000..5d0fe51
--- /dev/null
+++ b/test/intersect/chromsOutOfOrder.bed
@@ -0,0 +1,4 @@
+chr1 100 200
+chr1 150 250
+chr2 100 200
+chr1 200 300
diff --git a/test/intersect/d.bed b/test/intersect/d.bed
new file mode 100644
index 0000000..27061a4
--- /dev/null
+++ b/test/intersect/d.bed
@@ -0,0 +1 @@
+chr1 5 15
diff --git a/test/intersect/gdc.bam b/test/intersect/gdc.bam
new file mode 100644
index 0000000..80dcfaa
Binary files /dev/null and b/test/intersect/gdc.bam differ
diff --git a/test/intersect/gdc.gff b/test/intersect/gdc.gff
new file mode 100644
index 0000000..4777534
--- /dev/null
+++ b/test/intersect/gdc.gff
@@ -0,0 +1,12 @@
+chr2L . UTR 41 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
+chr2L . CDS 71 130 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
+chr2L . intron 131 170 0 + . ID=mRNA:xs2:intron:131-170;Parent=mRNA:xs2;
+chr2L . CDS 171 200 0 + . ID=mRNA:xs2:CDS:171-200;Parent=mRNA:xs2;
+chr2L . UTR 201 220 0 + . ID=mRNA:xs2:UTR:201-220;Parent=mRNA:xs2;
+chr2L . exon 41 130 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
+chr2L . exon 171 220 0 + . ID=mRNA:xs2:exon:171-220;Parent=mRNA:xs2;
+chr2L . mRNA 41 220 0 + . ID=mRNA:xs2;Parent=g2;
+chr2L . CDS 161 230 0 - . ID=tRNA:t2:CDS:161-230;Parent=tRNA:t2;
+chr2L . exon 161 230 0 - . ID=tRNA:t2:exon:161-230;Parent=tRNA:t2;
+chr2L . tRNA 161 230 0 - . ID=tRNA:t2;Parent=t2;
+chr2L . gene 41 220 0 + . ID=g2;
diff --git a/test/intersect/gdc_exp b/test/intersect/gdc_exp
new file mode 100644
index 0000000..442b7f2
--- /dev/null
+++ b/test/intersect/gdc_exp
@@ -0,0 +1,12 @@
+chr2L 10 15 None 255 + 10 15 0,0,0 1 5, 0,
+chr2L 70 75 None 255 - 70 75 0,0,0 1 5, 0,
+chr2L 70 75 None 255 - 70 75 0,0,0 1 5, 0,
+chr2L 140 145 None 255 - 140 145 0,0,0 1 5, 0,
+chr2L 140 145 None 255 - 140 145 0,0,0 1 5, 0,
+chr2L 150 155 None 255 - 150 155 0,0,0 1 5, 0,
+chr2L 210 215 None 255 + 210 215 0,0,0 1 5, 0,
+chr2L 70 75 None 255 + 70 75 0,0,0 1 5, 0,
+chr2L 70 75 None 255 + 70 75 0,0,0 1 5, 0,
+chr2L 140 145 None 255 + 140 145 0,0,0 1 5, 0,
+chr2L 140 145 None 255 + 140 145 0,0,0 1 5, 0,
+chr2L 160 165 None 255 + 160 165 0,0,0 1 5, 0,
diff --git a/test/intersect/gdc_one.bed b/test/intersect/gdc_one.bed
new file mode 100644
index 0000000..3777329
--- /dev/null
+++ b/test/intersect/gdc_one.bed
@@ -0,0 +1 @@
+chr2L 50 100
diff --git a/test/intersect/human.hg19.genome b/test/intersect/human.hg19.genome
new file mode 100644
index 0000000..d22ce2d
--- /dev/null
+++ b/test/intersect/human.hg19.genome
@@ -0,0 +1,94 @@
+
+chr1 249250621
+chr10 135534747
+chr11 135006516
+chr11_gl000202_random 40103
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr17_ctg5_hap1 1680828
+chr17_gl000203_random 37498
+chr17_gl000204_random 81310
+chr17_gl000205_random 174588
+chr17_gl000206_random 41001
+chr18 78077248
+chr18_gl000207_random 4262
+chr19 59128983
+chr19_gl000208_random 92689
+chr19_gl000209_random 159169
+chr1_gl000191_random 106433
+chr1_gl000192_random 547496
+chr2 243199373
+chr20 63025520
+chr21 48129895
+chr21_gl000210_random 27682
+chr22 51304566
+chr3 198022430
+chr4 191154276
+chr4_ctg9_hap1 590426
+chr4_gl000193_random 189789
+chr4_gl000194_random 191469
+chr5 180915260
+chr6 171115067
+chr6_apd_hap1 4622290
+chr6_cox_hap2 4795371
+chr6_dbb_hap3 4610396
+chr6_mann_hap4 4683263
+chr6_mcf_hap5 4833398
+chr6_qbl_hap6 4611984
+chr6_ssto_hap7 4928567
+chr7 159138663
+chr7_gl000195_random 182896
+chr8 146364022
+chr8_gl000196_random 38914
+chr8_gl000197_random 37175
+chr9 141213431
+chr9_gl000198_random 90085
+chr9_gl000199_random 169874
+chr9_gl000200_random 187035
+chr9_gl000201_random 36148
+chrM 16571
+chrUn_gl000211 166566
+chrUn_gl000212 186858
+chrUn_gl000213 164239
+chrUn_gl000214 137718
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chrUn_gl000218 161147
+chrUn_gl000219 179198
+chrUn_gl000220 161802
+chrUn_gl000221 155397
+chrUn_gl000222 186861
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000225 211173
+chrUn_gl000226 15008
+chrUn_gl000227 128374
+chrUn_gl000228 129120
+chrUn_gl000229 19913
+chrUn_gl000230 43691
+chrUn_gl000231 27386
+chrUn_gl000232 40652
+chrUn_gl000233 45941
+chrUn_gl000234 40531
+chrUn_gl000235 34474
+chrUn_gl000236 41934
+chrUn_gl000237 45867
+chrUn_gl000238 39939
+chrUn_gl000239 33824
+chrUn_gl000240 41933
+chrUn_gl000241 42152
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000244 39929
+chrUn_gl000245 36651
+chrUn_gl000246 38154
+chrUn_gl000247 36422
+chrUn_gl000248 39786
+chrUn_gl000249 38502
+chrX 155270560
+chrY 59373566
diff --git a/test/intersect/human.hg19.vSort.genome b/test/intersect/human.hg19.vSort.genome
new file mode 100644
index 0000000..ae5e9d3
--- /dev/null
+++ b/test/intersect/human.hg19.vSort.genome
@@ -0,0 +1,93 @@
+chr1 249250621
+chr2 243199373
+chr3 198022430
+chr4 191154276
+chr5 180915260
+chr6 171115067
+chr7 159138663
+chr8 146364022
+chr9 141213431
+chr10 135534747
+chr11 135006516
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr18 78077248
+chr19 59128983
+chr20 63025520
+chr21 48129895
+chr22 51304566
+chrX 155270560
+chrY 59373566
+chrM 16571
+chr1_gl000191_random 106433
+chr1_gl000192_random 547496
+chr4_ctg9_hap1 590426
+chr4_gl000193_random 189789
+chr4_gl000194_random 191469
+chr6_apd_hap1 4622290
+chr6_cox_hap2 4795371
+chr6_dbb_hap3 4610396
+chr6_mann_hap4 4683263
+chr6_mcf_hap5 4833398
+chr6_qbl_hap6 4611984
+chr6_ssto_hap7 4928567
+chr7_gl000195_random 182896
+chr8_gl000196_random 38914
+chr8_gl000197_random 37175
+chr9_gl000198_random 90085
+chr9_gl000199_random 169874
+chr9_gl000200_random 187035
+chr9_gl000201_random 36148
+chr11_gl000202_random 40103
+chr17_ctg5_hap1 1680828
+chr17_gl000203_random 37498
+chr17_gl000204_random 81310
+chr17_gl000205_random 174588
+chr17_gl000206_random 41001
+chr18_gl000207_random 4262
+chr19_gl000208_random 92689
+chr19_gl000209_random 159169
+chr21_gl000210_random 27682
+chrUn_gl000211 166566
+chrUn_gl000212 186858
+chrUn_gl000213 164239
+chrUn_gl000214 137718
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chrUn_gl000218 161147
+chrUn_gl000219 179198
+chrUn_gl000220 161802
+chrUn_gl000221 155397
+chrUn_gl000222 186861
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000225 211173
+chrUn_gl000226 15008
+chrUn_gl000227 128374
+chrUn_gl000228 129120
+chrUn_gl000229 19913
+chrUn_gl000230 43691
+chrUn_gl000231 27386
+chrUn_gl000232 40652
+chrUn_gl000233 45941
+chrUn_gl000234 40531
+chrUn_gl000235 34474
+chrUn_gl000236 41934
+chrUn_gl000237 45867
+chrUn_gl000238 39939
+chrUn_gl000239 33824
+chrUn_gl000240 41933
+chrUn_gl000241 42152
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000244 39929
+chrUn_gl000245 36651
+chrUn_gl000246 38154
+chrUn_gl000247 36422
+chrUn_gl000248 39786
+chrUn_gl000249 38502
diff --git a/test/intersect/j1.bed b/test/intersect/j1.bed
new file mode 100644
index 0000000..296a676
--- /dev/null
+++ b/test/intersect/j1.bed
@@ -0,0 +1 @@
+chr1 98650 98750 a1 100 +
diff --git a/test/intersect/new_test-intersect.sh b/test/intersect/new_test-intersect.sh
new file mode 100755
index 0000000..4bdcdf0
--- /dev/null
+++ b/test/intersect/new_test-intersect.sh
@@ -0,0 +1,668 @@
+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
+$BT intersect -a nonExistantFile.bed -b b.bed -sorted 2>&1 > /dev/null | cat - >obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test that we throw an error for empty files
+############################################################
+echo " intersect.new.t51...\c"
+echo "is an empty file." > exp
+touch dummy.txt
+$BT intersect -a dummy.txt -b b.bed 2>&1 > /dev/null | cut -f3-6 -d ' ' > 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
+
+
+
diff --git a/test/intersect/oneUnmapped.bam b/test/intersect/oneUnmapped.bam
new file mode 100644
index 0000000..9bac213
Binary files /dev/null and b/test/intersect/oneUnmapped.bam differ
diff --git a/test/intersect/performanceTest.sh b/test/intersect/performanceTest.sh
new file mode 100755
index 0000000..6e91093
--- /dev/null
+++ b/test/intersect/performanceTest.sh
@@ -0,0 +1,138 @@
+#################################################################
+#
+# PERFORMANCE TESTS FOR VARIOUS INPUT METHODS.
+#
+# We'll test uncompressed data, gzip, bgzip, and Bam files.
+# Each will be tried as a file, and as the 3 types of stdin:
+# redirects, pipes, and fifos.
+#
+# We'll run each one twice in a row to check for improvement
+# due to a cache warm up.
+#
+#################################################################
+
+
+BT=${BT-../../bin/bedtools}
+
+
+#################################################################
+# Start by generating data, if desired
+#
+#################################################################
+if true; then
+ echo "generating data..."
+ mkdir perfData
+ cd perfData
+ ../$BT random -l 1000 -n 20000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed
+ ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed
+ cp a10M.bed a10M_gzipped.bed
+ gzip a10M_gzipped.bed
+ cp a10M.bed a10M_bgzipped.bed
+ bgzip a10M_bgzipped.bed
+ ../$BT bedtobam -i a10M.bed -g ../human.hg19.genome > a10M.bam
+ cd ..
+fi
+
+###################################################################
+# Begin Tests
+###################################################################
+echo -e "Test 1 of 16...."
+echo "Test 1: Intersect a10M, ten million records, uncompressed from file with b10M" > runLog.txt
+runit $BT intersect -a perfData/a10M.bed -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 1 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M.bed -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 2 of 16...."
+echo -e "\n\nTest 2: Intersect a10M, ten million records, gzipped from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M_gzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 2 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M_gzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 3 of 16...."
+echo -e "\n\nTest 3: Intersect a10M, ten million records, bgzipped from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M_bgzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 3 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M_bgzipped.bed.gz -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 4 of 16...."
+echo -e "\n\nTest 4: Intersect a10M, ten million records, bam from file with b10M" >> runLog.txt
+runit $BT intersect -a perfData/a10M.bam -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 4 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a perfData/a10M.bam -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+
+echo -e "Test 5 of 16...."
+echo -e "\n\nTest 5: Intersect a10M, ten million records, uncompressed from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bed 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 5 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bed 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 6 of 16...."
+echo -e "\n\nTest 6: Intersect a10M, ten million records, gzipped from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_gzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 6 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_gzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 7 of 16...."
+echo -e "\n\nTest 7: Intersect a10M, ten million records, bgzipped from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_bgzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 7 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M_bgzipped.bed.gz 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 8 of 16...."
+echo -e "\n\nTest 8: Intersect a10M, ten million records, bam from redirect with b10M" >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bam 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 8 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a - -b perfData/b10M.bed -sorted < perfData/a10M.bam 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 9 of 16...."
+echo -e "\n\nTest 9: Intersect a10M, ten million records, uncompressed from pipe with b10M" >> runLog.txt
+cat perfData/a10M.bed | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 9 for possible cache speed up." >> runLog.txt
+cat perfData/a10M.bed | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 10 of 16...."
+echo -e "\n\nTest 10: Intersect a10M, ten million records, gzip from pipe with b10M" >> runLog.txt
+cat perfData/a10M_gzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 10 for possible cache speed up." >> runLog.txt
+cat perfData/a10M_gzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 11 of 16...."
+echo -e "\n\nTest 11: Intersect a10M, ten million records, bgzip from pipe with b10M" >> runLog.txt
+cat perfData/a10M_bgzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 11 for possible cache speed up." >> runLog.txt
+cat perfData/a10M_bgzipped.bed.gz | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 12 of 16...."
+echo -e "\n\nTest 12: Intersect a10M, ten million records, bam from pipe with b10M" >> runLog.txt
+cat perfData/a10M.bam | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 12 for possible cache speed up." >> runLog.txt
+cat perfData/a10M.bam | runit $BT intersect -a - -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 13 of 16...."
+echo -e "\n\nTest 13: Intersect a10M, ten million records, uncompressed from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bed) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 13 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bed) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 14 of 16...."
+echo -e "\n\nTest 14: Intersect a10M, ten million records, gzipped from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_gzipped.bed.gz) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 14 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_gzipped.bed.gz) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 15 of 16...."
+echo -e "\n\nTest 15: Intersect a10M, ten million records, bgzipped from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_bgzipped.bed.gz) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 15 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M_bgzipped.bed.gz) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+echo -e "Test 16 of 16...."
+echo -e "\n\nTest 16: Intersect a10M, ten million records, bam from fifo with b10M" >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bam) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+echo -e "\nRe-do test 16 for possible cache speed up." >> runLog.txt
+runit $BT intersect -a <(cat perfData/a10M.bam) -b perfData/b10M.bed -sorted 2>&1 >/dev/null | grep -e "user" -e maxrss >> runLog.txt
+
+
+echo "Tests completed."
+rm -rf perfData
diff --git a/test/intersect/queryUnmappedMateMappedCoordsInvalid.bam b/test/intersect/queryUnmappedMateMappedCoordsInvalid.bam
new file mode 100644
index 0000000..1ecaaae
Binary files /dev/null and b/test/intersect/queryUnmappedMateMappedCoordsInvalid.bam differ
diff --git a/test/intersect/recordsOutOfOrder.bed b/test/intersect/recordsOutOfOrder.bed
new file mode 100644
index 0000000..8ff0d0b
--- /dev/null
+++ b/test/intersect/recordsOutOfOrder.bed
@@ -0,0 +1,4 @@
+chr1 20 30
+chr1 40 50
+chr1 15 60
+chr1 70 80
diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh
index cfd1079..da0ba96 100644
--- a/test/intersect/test-intersect.sh
+++ b/test/intersect/test-intersect.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -129,6 +129,7 @@ $BT intersect -a a.bed -b b.bed -wo -s > obs
check obs exp
rm obs exp
+
###########################################################
# Test with -wao (write all overlap) with -s
############################################################
@@ -255,6 +256,67 @@ rm obs exp
+###########################################################
+# Test three blocks with -split -wo only shows 5 overlap
+# bases, not ten.
+############################################################
+echo " intersect.t22.a...\c"
+echo "chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40, chr1 5 15 5" > exp
+$BT intersect -a three_blocks_match.bed -b d.bed -split -wo > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Same test but for BAM file
+############################################################
+echo " intersect.t22.b...\c"
+echo "chr1 0 50 three_blocks_match 255 + 0 50 0,0,0 3 10,10,10, 0,20,40, chr1 5 15 5" > exp
+$BT intersect -a three_blocks_match.bam -b d.bed -split -wo -bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test three blocks with -split -wo, and DB record also has
+# blocks that somewhat intersect
+############################################################
+echo " intersect.t22.c...\c"
+echo "chr1 0 50 three_blocks_match 0 + 0 0 0 3 10,10,10, 0,20,40, chr1 0 45 three_blocks_match 0 + 0 0 0 2 5,10, 25,35, 10" > exp
+$BT intersect -a three_blocks_match.bed -b two_blocks_partial.bed -split -wo > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Same test but for BAM file
+############################################################
+echo " intersect.t22.d...\c"
+echo "chr1 0 50 three_blocks_match 255 + 0 50 0,0,0 3 10,10,10, 0,20,40, chr1 0 45 three_blocks_match 0 + 0 0 0 2 5,10, 25,35, 10" > exp
+$BT intersect -a three_blocks_match.bam -b two_blocks_partial.bed -split -wo -bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test three blocks with -split -wo, and DB record also has
+# blocks that do not intersect
+############################################################
+echo " intersect.t22.e...\c"
+touch exp
+$BT intersect -a three_blocks_match.bed -b three_blocks_nomatch.bed -split -wo > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Same test but for BAM file
+############################################################
+echo " intersect.t22.f...\c"
+touch exp
+$BT intersect -a three_blocks_match.bam -b three_blocks_nomatch.bed -split -wo -bed > obs
+check obs exp
+rm obs exp
+
+
+
##################################################################
# Test that only the mapped read is is found as an intersection
##################################################################
@@ -281,7 +343,7 @@ rm obs exp
echo " intersect.t25...\c"
echo \
"chr1 0 30 one_blocks 40 - 0 30 0,0,0 1 30, 0, 1" > exp
-$BT intersect -abam one_block.bam -b c.bed -c > obs
+$BT intersect -abam one_block.bam -b c.bed -c -bed > obs
check obs exp
rm obs exp
@@ -291,7 +353,7 @@ rm obs exp
echo " intersect.t26...\c"
echo \
"chr1 0 30 one_blocks 40 - 0 30 0,0,0 1 30, 0, chr1 0 100 c1 1 + 30" > exp
-$BT intersect -abam one_block.bam -b c.bed -wo > obs
+$BT intersect -abam one_block.bam -b c.bed -wo -bed > obs
check obs exp
rm obs exp
@@ -301,10 +363,90 @@ rm obs exp
echo " intersect.t27...\c"
echo \
"chr1 0 30 one_blocks 40 - 0 30 0,0,0 1 30, 0, chr1 0 100 c1 1 + 30" > exp
-$BT intersect -abam one_block.bam -b c.bed -wo > obs
+$BT intersect -abam one_block.bam -b c.bed -wo -bed > obs
check obs exp
+##################################################################
+# Test BED3 with BED3
+##################################################################
+echo " intersect.t28...\c"
+echo \
+"chr1^I10^I20^Ichr1^I10^I20" > exp
+$BT intersect -a bed3.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test BED4 with BED3
+##################################################################
+echo " intersect.t29...\c"
+echo \
+"chr1^I10^I20^I345.7^Ichr1^I10^I20" > exp
+$BT intersect -a bed4.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test BED5 with BED3
+##################################################################
+echo " intersect.t30...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^Ichr1^I10^I20" > exp
+$BT intersect -a bed5.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test BED6 (without a proper strand) with BED3
+##################################################################
+echo " intersect.t31...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I11^Ichr1^I10^I20" > exp
+$BT intersect -a bed6.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test BED6 (with a strand) with BED3
+##################################################################
+echo " intersect.t32...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I10^I20" > exp
+$BT intersect -a bed6.strand.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test BED PLUS with BED3
+##################################################################
+echo " intersect.t33...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I11^Ifoo^Ibar^Ibiz^I11^Ibang^Ibop^I99^Ichr1^I10^I20" > exp
+$BT intersect -a bedplus.bed -b bed3.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test for strand matches with BED3
+##################################################################
+echo " intersect.t34...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I11^Ichr1^I10^I20^I345.7^Iwhy?^I-" > exp
+$BT intersect -a bed6.bed -b bed6.strand.bed -wa -wb | cat -t > obs
+check obs exp
+
+##################################################################
+# Test for strand matches with BED3
+##################################################################
+echo " intersect.t35...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I10^I20^I345.7^Iwhy?^I-" > exp
+$BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -s | cat -t > obs
+check obs exp
+
+##################################################################
+# Test for strand matches with BED3
+##################################################################
+echo " intersect.t36...\c"
+echo \
+"chr1^I10^I20^I345.7^Iwhy?^I-^Ichr1^I11^I21^I345.7^Iwhy?^I+" > exp
+$BT intersect -a bed6.strand.bed -b bed6.strand2.bed -wa -wb -S | cat -t > obs
+check obs exp
rm obs exp
-rm *.bam
\ No newline at end of file
+rm one_block.bam two_blocks.bam three_blocks.bam
\ No newline at end of file
diff --git a/test/intersect/three_blocks_match.bam b/test/intersect/three_blocks_match.bam
new file mode 100644
index 0000000..f67547b
Binary files /dev/null and b/test/intersect/three_blocks_match.bam differ
diff --git a/test/intersect/two_blocks_partial.bam b/test/intersect/two_blocks_partial.bam
new file mode 100644
index 0000000..3a82822
Binary files /dev/null and b/test/intersect/two_blocks_partial.bam differ
diff --git a/test/intersect/two_blocks_partial.bed b/test/intersect/two_blocks_partial.bed
new file mode 100644
index 0000000..8a83f35
--- /dev/null
+++ b/test/intersect/two_blocks_partial.bed
@@ -0,0 +1 @@
+chr1 0 45 three_blocks_match 0 + 0 0 0 2 5,10, 25,35,
diff --git a/test/jaccard/test-jaccard.sh b/test/jaccard/test-jaccard.sh
index e44dc04..587b924 100644
--- a/test/jaccard/test-jaccard.sh
+++ b/test/jaccard/test-jaccard.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -11,11 +11,11 @@ check()
###########################################################
# Test a basic self intersection
-############################################################
+###########################################################
echo " jaccard.t01...\c"
echo \
-"intersection union jaccard
-110 110 1" > exp
+"intersection union-intersection jaccard n_intersections
+110 110 1 2" > exp
$BT jaccard -a a.bed -b a.bed > obs
check obs exp
rm obs exp
@@ -23,16 +23,16 @@ rm obs exp
echo " jaccard.t02...\c"
echo \
-"intersection union jaccard
-10 140 0.0714286" > exp
+"intersection union-intersection jaccard n_intersections
+10 140 0.0714286 1" > exp
$BT jaccard -a a.bed -b b.bed > obs
check obs exp
rm obs exp
echo " jaccard.t03...\c"
echo \
-"intersection union jaccard
-10 200 0.05" > exp
+"intersection union-intersection jaccard n_intersections
+10 200 0.05 1" > exp
$BT jaccard -a a.bed -b c.bed > obs
check obs exp
rm obs exp
@@ -40,8 +40,30 @@ rm obs exp
echo " jaccard.t04...\c"
echo \
-"intersection union jaccard
-0 210 0" > exp
-$BT jaccard -a a.bed -b b.bed > obs
+"intersection union-intersection jaccard n_intersections
+0 210 0 0" > exp
+$BT jaccard -a a.bed -b d.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test stdin
+###########################################################
+echo " jaccard.t05...\c"
+echo \
+"intersection union-intersection jaccard n_intersections
+10 140 0.0714286 1" > exp
+cat a.bed | $BT jaccard -a - -b b.bed > obs
check obs exp
-rm obs exp
\ No newline at end of file
+rm obs exp
+
+
+###########################################################
+# Test symmetry
+###########################################################
+echo " jaccard.t06...\c"
+$BT jaccard -a a.bed -b b.bed > obs1
+$BT jaccard -a b.bed -b a.bed > obs2
+check obs1 obs2
+
+rm obs1 obs2
diff --git a/test/map/a.vsorted.bed b/test/map/a.vsorted.bed
new file mode 100644
index 0000000..6b32d0c
--- /dev/null
+++ b/test/map/a.vsorted.bed
@@ -0,0 +1,5 @@
+chr1 10 20
+chr2 10 20
+chr2 200 300
+chr10 10 20
+chr10 20 30
\ No newline at end of file
diff --git a/test/map/b.vsorted.bed b/test/map/b.vsorted.bed
new file mode 100644
index 0000000..83698f4
--- /dev/null
+++ b/test/map/b.vsorted.bed
@@ -0,0 +1,3 @@
+chr1 11 20
+chr2 11 20
+chr10 11 20
\ No newline at end of file
diff --git a/test/map/genome b/test/map/genome
new file mode 100644
index 0000000..6085f58
--- /dev/null
+++ b/test/map/genome
@@ -0,0 +1,3 @@
+chr1 1000
+chr2 1000
+chr10 1000
\ No newline at end of file
diff --git a/test/map/ivls.bed b/test/map/ivls.bed
index b7027f5..44cc9c4 100644
--- a/test/map/ivls.bed
+++ b/test/map/ivls.bed
@@ -1,3 +1,4 @@
+#header
chr1 0 100
chr1 100 200
chr2 0 100
diff --git a/test/map/ivls2.bed b/test/map/ivls2.bed
new file mode 100644
index 0000000..d47c834
--- /dev/null
+++ b/test/map/ivls2.bed
@@ -0,0 +1,3 @@
+chr1 0 10 a1 10 -
+chr2 10 20 a7 2 +
+chr3 120 130 a9 4 -
\ No newline at end of file
diff --git a/test/map/t.bed b/test/map/t.bed
new file mode 100644
index 0000000..d6c80bc
--- /dev/null
+++ b/test/map/t.bed
@@ -0,0 +1 @@
+chr1 10 20
diff --git a/test/map/test-map.sh b/test/map/test-map.sh
index 7fc286b..293d84e 100644
--- a/test/map/test-map.sh
+++ b/test/map/test-map.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -131,3 +131,554 @@ $BT map -a ivls.bed -b values2.bed -o antimode > obs
check obs exp
rm obs exp
+
+###########################################################
+# Test column extraction from BEDPLUS
+############################################################
+echo " map.t09...\c"
+echo \
+"chr1 0 100 1,2,3,4,5,-6
+chr1 100 200 7
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 8,9,-10
+chr3 100 200 11,12" > exp
+$BT map -a ivls.bed -b values4.bed -c 7 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test min
+############################################################
+echo " map.t10...\c"
+echo \
+"chr1 0 100 -6
+chr1 100 200 7
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 -10
+chr3 100 200 11" > exp
+$BT map -a ivls.bed -b values4.bed -c 7 -o min > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test absmin
+############################################################
+echo " map.t11...\c"
+echo \
+"chr1 0 100 1
+chr1 100 200 7
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 8
+chr3 100 200 11" > exp
+$BT map -a ivls.bed -b values4.bed -c 7 -o absmin > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test max
+############################################################
+echo " map.t12...\c"
+echo \
+"chr1 0 100 5
+chr1 100 200 7
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 9
+chr3 100 200 12" > exp
+$BT map -a ivls.bed -b values4.bed -c 7 -o max > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test absmax
+############################################################
+echo " map.t13...\c"
+echo \
+"chr1 0 100 6
+chr1 100 200 7
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 10
+chr3 100 200 12" > exp
+$BT map -a ivls.bed -b values4.bed -c 7 -o absmax > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t14...\c"
+echo \
+"chr1 0 100 chr1,chr1,chr1,chr1,chr1
+chr1 100 200 chr1
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 1 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t15...\c"
+echo \
+"chr1 0 100 hg19_ccdsGene,hg19_ccdsGene,hg19_ccdsGene,hg19_ccdsGene,hg19_ccdsGene
+chr1 100 200 hg19_ccdsGene
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 2 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t16...\c"
+echo \
+"chr1 0 100 start_codon,CDS,exon,CDS,exon
+chr1 100 200 exon
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 3 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t17...\c"
+echo \
+"chr1 0 100 1,2,8,9,40
+chr1 100 200 40
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 4 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t18...\c"
+echo \
+"chr1 0 100 9,11,20,17,200
+chr1 100 200 200
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 5 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t19...\c"
+echo \
+"chr1 0 100 0.000000,0.000000,0.000000,0.000000,0.000000
+chr1 100 200 0.000000
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 6 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t20...\c"
+echo \
+"chr1 0 100 +,+,+,+,+
+chr1 100 200 +
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 7 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t21...\c"
+echo \
+"chr1 0 100 .,0,.,2,.
+chr1 100 200 .
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 8 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test GFF column extraction
+############################################################
+echo " map.t22..\c"
+echo \
+"chr1 0 100 gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";,gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";,gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";,gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";,gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";
+chr1 100 200 gene_id \"CCDS30744.1\"; transcript_id \"CCDS30744.1\";
+chr2 0 100 .
+chr2 100 200 .
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.gff -c 9 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t23..\c"
+echo \
+"chr1 0 100 chr1,chr1,chr1
+chr1 100 200 chr1,chr1
+chr2 0 100 .
+chr2 100 200 chr2,chr2
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 1 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t24..\c"
+echo \
+"chr1 0 100 10,15,20
+chr1 100 200 110,130
+chr2 0 100 .
+chr2 100 200 110,130
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 2 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t25..\c"
+echo \
+"chr1 0 100 rs6054257,.,rs6040355
+chr1 100 200 .,microsat1
+chr2 0 100 .
+chr2 100 200 .,microsat1
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 3 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t26..\c"
+echo \
+"chr1 0 100 G,T,A
+chr1 100 200 T,GTC
+chr2 0 100 .
+chr2 100 200 T,GTC
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 4 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t27..\c"
+echo \
+"chr1 0 100 A,A,G,T
+chr1 100 200 .,G,GTCT
+chr2 0 100 .
+chr2 100 200 .,G,GTCT
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 5 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t28..\c"
+echo \
+"chr1 0 100 29,3,67
+chr1 100 200 47,50
+chr2 0 100 .
+chr2 100 200 47,50
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 6 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t29..\c"
+echo \
+"chr1 0 100 PASS,q10,PASS
+chr1 100 200 PASS,PASS
+chr2 0 100 .
+chr2 100 200 PASS,PASS
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 7 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t30..\c"
+echo \
+"chr1 0 100 NS=3;DP=14;AF=0.5;DB;H2,NS=3;DP=11;AF=0.017,NS=2;DP=10;AF=0.333,0.667;AA=T;DB
+chr1 100 200 NS=3;DP=13;AA=T,NS=3;DP=9;AA=G
+chr2 0 100 .
+chr2 100 200 NS=3;DP=13;AA=T,NS=3;DP=9;AA=G
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 8 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t31..\c"
+echo \
+"chr1 0 100 GT:GQ:DP:HQ,GT:GQ:DP:HQ,GT:GQ:DP:HQ
+chr1 100 200 GT:GQ:DP:HQ,GT:GQ:DP
+chr2 0 100 .
+chr2 100 200 GT:GQ:DP:HQ,GT:GQ:DP
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 9 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t32..\c"
+echo \
+"chr1 0 100 0|0:48:1:51,51,0|0:49:3:58,50,1|2:21:6:23,27
+chr1 100 200 0|0:54:7:56,60,0/1:35:4
+chr2 0 100 .
+chr2 100 200 0|0:54:7:56,60,0/1:35:4
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -c 10 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test VCF column extraction
+############################################################
+echo " map.t33..\c"
+echo \
+"
+*****
+*****ERROR: requested column 15 , but record only has fields 1 - 12. Exiting.
+
+*****" > exp
+$BT map -a ivls.bed -b test.vcf -c 15 -o collapse 2> obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test -header
+############################################################
+echo " map.t33..\c"
+echo \
+"#header
+chr1 0 100 0|0:48:1:51,51,0|0:49:3:58,50,1|2:21:6:23,27
+chr1 100 200 0|0:54:7:56,60,0/1:35:4
+chr2 0 100 .
+chr2 100 200 0|0:54:7:56,60,0/1:35:4
+chr3 0 100 .
+chr3 100 200 ." > exp
+$BT map -a ivls.bed -b test.vcf -header -c 10 -o collapse > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test -null
+############################################################
+echo " map.t33..\c"
+echo \
+"chr1 0 100 0|0:48:1:51,51,0|0:49:3:58,50,1|2:21:6:23,27
+chr1 100 200 0|0:54:7:56,60,0/1:35:4
+chr2 0 100 NULL
+chr2 100 200 0|0:54:7:56,60,0/1:35:4
+chr3 0 100 NULL
+chr3 100 200 NULL" > exp
+$BT map -a ivls.bed -b test.vcf -null NULL -c 10 -o collapse > obs
+check obs exp
+
+###########################################################
+# Test -s
+############################################################
+echo " map.t34..\c"
+echo \
+"chr1 0 10 a1 10 - .
+chr2 10 20 a7 2 + .
+chr3 120 130 a9 4 - ." > exp
+$BT map -a ivls2.bed -b values.bed -c 4 -o collapse -s > obs
+check obs exp
+
+###########################################################
+# Test -S
+############################################################
+echo " map.t35..\c"
+echo \
+"chr1 0 10 a1 10 - a1
+chr2 10 20 a7 2 + .
+chr3 120 130 a9 4 - a8" > exp
+$BT map -a ivls2.bed -b values.bed -c 4 -o collapse -S > obs
+check obs exp
+
+###########################################################
+# Test -f 0.1
+############################################################
+echo " map.t36..\c"
+echo \
+"chr1 0 10 a1 10 - a1
+chr2 10 20 a7 2 + .
+chr3 120 130 a9 4 - a8" > exp
+$BT map -a ivls2.bed -b values5.bed -c 4 -o collapse -f 0.1 > obs
+check obs exp
+
+###########################################################
+# Test -f 0.7
+############################################################
+echo " map.t37..\c"
+echo \
+"chr1 0 10 a1 10 - .
+chr2 10 20 a7 2 + .
+chr3 120 130 a9 4 - a8" > exp
+$BT map -a ivls2.bed -b values5.bed -c 4 -o collapse -f 0.7 > obs
+check obs exp
+
+###########################################################
+# Test -f 0.9
+############################################################
+echo " map.t38..\c"
+echo \
+"chr1 0 10 a1 10 - .
+chr2 10 20 a7 2 + .
+chr3 120 130 a9 4 - ." > exp
+$BT map -a ivls2.bed -b values5.bed -c 4 -o collapse -f 0.9 > obs
+check obs exp
+
+###########################################################
+# Test -g
+############################################################
+echo " map.t39..\c"
+echo \
+"chr1 10 20 chr1
+chr2 10 20 chr2
+chr2 200 300 .
+chr10 10 20 .
+chr10 20 30 ." > exp
+$BT map -a a.vsorted.bed -b b.vsorted.bed -c 1 -o collapse > obs
+check obs exp
+
+###########################################################
+# Test -g
+############################################################
+echo " map.t40..\c"
+echo \
+"chr1 10 20 chr1
+chr2 10 20 chr2
+chr2 200 300 .
+chr10 10 20 chr10
+chr10 20 30 ." > exp
+$BT map -g genome -a a.vsorted.bed -b b.vsorted.bed -c 1 -o collapse > obs
+check obs exp
+
+###########################################################
+# Test invalid column
+############################################################
+echo " map.t41..\c"
+echo \
+"
+*****
+*****ERROR: requested column 41 , but record only has fields 1 - 6. Exiting.
+
+*****" > exp
+$BT map -a ivls.bed -b values5.bed -c 41 -o collapse 2> obs
+check obs exp
+
+rm obs exp
+
+###########################################################
+# Test invalid column
+############################################################
+echo " map.t42..\c"
+echo \
+"
+*****
+*****ERROR: requested column -1 , but record only has fields 1 - 6. Exiting.
+
+*****" > exp
+$BT map -a ivls.bed -b values5.bed -c -1 -o collapse 2> obs
+check obs exp
+
+rm obs exp
+
+###########################################################
+# Test invalid column
+############################################################
+echo " map.t43..\c"
+echo \
+"
+*****
+*****ERROR: requested column 0 , but record only has fields 1 - 6. Exiting.
+
+*****" > exp
+$BT map -a ivls.bed -b values5.bed -c 0 -o collapse 2> obs
+check obs exp
+
+rm obs exp
+
+
+###########################################################
+# Test that Bam database is not allowed
+############################################################
+echo " map.t44...\c"
+echo -e "\n*****\n***** ERROR: BAM database file not currently supported for the map tool." > exp
+$BT map -a ivls.bed -b values.bam 2> obs
+check obs exp
+rm obs exp
+
+
+
+###########################################################
+# Test that -split option works correctly
+############################################################
+echo " map.t45...\c"
+echo "chr1 0 50 three_blocks_match 15 + 0 0 0 3 10,10,10, 0,20,40, ." > exp
+$BT map -o sum -a three_blocks_match.bed -b three_blocks_nomatch.bed -split > obs
+check obs exp
+rm obs exp
diff --git a/test/map/test.gff b/test/map/test.gff
new file mode 100644
index 0000000..9d9b680
--- /dev/null
+++ b/test/map/test.gff
@@ -0,0 +1,7 @@
+chr1 hg19_ccdsGene start_codon 1 9 0.000000 + . gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
+chr1 hg19_ccdsGene CDS 2 11 0.000000 + 0 gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
+chr1 hg19_ccdsGene exon 8 20 0.000000 + . gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
+chr1 hg19_ccdsGene CDS 9 17 0.000000 + 2 gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
+chr1 hg19_ccdsGene exon 40 200 0.000000 + . gene_id "CCDS30744.1"; transcript_id "CCDS30744.1";
+
+
diff --git a/test/map/test.vcf b/test/map/test.vcf
new file mode 100644
index 0000000..ba14a79
--- /dev/null
+++ b/test/map/test.vcf
@@ -0,0 +1,26 @@
+##fileformat=VCFv4.1
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+chr1 10 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+chr1 15 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
+chr1 20 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
+chr1 110 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
+chr1 130 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
+chr2 110 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
+chr2 130 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
diff --git a/test/map/three_blocks_match.bed b/test/map/three_blocks_match.bed
new file mode 100644
index 0000000..e4004fa
--- /dev/null
+++ b/test/map/three_blocks_match.bed
@@ -0,0 +1 @@
+chr1 0 50 three_blocks_match 15 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/map/three_blocks_nomatch.bed b/test/map/three_blocks_nomatch.bed
new file mode 100644
index 0000000..3db90e0
--- /dev/null
+++ b/test/map/three_blocks_nomatch.bed
@@ -0,0 +1 @@
+chr1 10 60 three_blocks_nomatch 25 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/map/values.bam b/test/map/values.bam
new file mode 100644
index 0000000..97caea3
Binary files /dev/null and b/test/map/values.bam differ
diff --git a/test/map/values.bed b/test/map/values.bed
index 3710f4c..74a0839 100644
--- a/test/map/values.bed
+++ b/test/map/values.bed
@@ -5,4 +5,4 @@ chr1 120 130 a4 1 +
chr3 0 10 a5 1 +
chr3 10 20 a6 2 +
chr3 20 30 a7 3 +
-chr3 120 130 a8 4 +
\ No newline at end of file
+chr3 120 130 a8 4 +
diff --git a/test/map/values4.bed b/test/map/values4.bed
new file mode 100644
index 0000000..5af672b
--- /dev/null
+++ b/test/map/values4.bed
@@ -0,0 +1,12 @@
+chr1 0 10 a1 10 + 1
+chr1 10 20 a2 5 + 2
+chr1 11 21 a3 5 + 3
+chr1 20 30 a4 15 + 4
+chr1 20 30 a5 15 + 5
+chr1 20 30 a6 15 + -6
+chr1 120 130 a7 1 + 7
+chr3 0 10 a8 1 + 8
+chr3 10 20 a9 2 + 9
+chr3 20 30 a10 3 + -10
+chr3 120 130 a11 4 + 11
+chr3 120 130 a12 4 + 12
diff --git a/test/map/values5.bed b/test/map/values5.bed
new file mode 100644
index 0000000..0c1ff27
--- /dev/null
+++ b/test/map/values5.bed
@@ -0,0 +1,8 @@
+chr1 4 10 a1 10 +
+chr1 14 20 a2 5 +
+chr1 26 30 a3 15 +
+chr1 127 130 a4 1 +
+chr3 0 10 a5 1 +
+chr3 15 20 a6 2 +
+chr3 22 30 a7 3 +
+chr3 122 130 a8 4 +
\ No newline at end of file
diff --git a/test/merge/test-merge.sh b/test/merge/test-merge.sh
index 91cf87d..ee7f629 100644
--- a/test/merge/test-merge.sh
+++ b/test/merge/test-merge.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -87,7 +87,7 @@ rm obs exp
echo " merge.t5...\c"
echo \
"chr1 10 20 a1
-chr1 30 100 a2;a3;a4" > exp
+chr1 30 100 a2,a3,a4" > exp
$BT merge -i a.names.bed -nms > obs
check obs exp
rm obs exp
@@ -98,10 +98,10 @@ rm obs exp
echo " merge.t6...\c"
echo \
"chr1 10 20 a1 1
-chr1 30 100 a2;a3;a4 9
+chr1 30 100 a2,a3,a4 9
chr2 10 20 a1 5
chr2 30 40 a2 6
-chr2 42 100 a3;a4 15" > exp
+chr2 42 100 a3,a4 15" > exp
$BT merge -i a.full.bed -nms -scores sum> obs
check obs exp
rm obs exp
@@ -126,10 +126,10 @@ rm obs exp
echo " merge.t8...\c"
echo \
"chr1 10 20 a1 1 1
-chr1 30 100 a2;a3;a4 9 3
+chr1 30 100 a2,a3,a4 9 3
chr2 10 20 a1 5 1
chr2 30 40 a2 6 1
-chr2 42 100 a3;a4 15 2" > exp
+chr2 42 100 a3,a4 15 2" > exp
$BT merge -i a.full.bed -nms -n -scores sum> obs
check obs exp
rm obs exp
@@ -150,3 +150,21 @@ chr2 45 100 a4 8 - 1" > exp
$BT merge -i a.full.bed -s -nms -n -scores sum> obs
check obs exp
rm obs exp
+
+###########################################################
+# Test #10
+# Test the use of a custom delimiter for -nms
+#
+# cat a.names.bed
+# chr1 10 20 a1
+# chr1 30 40 a2
+# chr1 40 50 a3
+# chr1 45 100 a4
+###########################################################
+echo " merge.t10...\c"
+echo \
+"chr1 10 20 a1
+chr1 30 100 a2|a3|a4" > exp
+$BT merge -i a.names.bed -nms -delim "|" > obs
+check obs exp
+rm obs exp
diff --git a/test/multicov/test-multicov.sh b/test/multicov/test-multicov.sh
index d2db630..c32ca92 100644
--- a/test/multicov/test-multicov.sh
+++ b/test/multicov/test-multicov.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/reldist/test-reldist.sh b/test/reldist/test-reldist.sh
new file mode 100644
index 0000000..eebde8b
--- /dev/null
+++ b/test/reldist/test-reldist.sh
@@ -0,0 +1,149 @@
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+# Test a basic self intersection. The relative distances
+# should all be 0 in this case.
+############################################################
+echo " reldist.t01...\c"
+echo \
+"reldist count total fraction
+0.00 43424 43424 1.000" > exp
+$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \
+ -b ../../data/refseq.chr1.exons.bed.gz > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test intervaks that are randomly distributed.
+# The relative distances should equally represented .
+############################################################
+echo " reldist.t02...\c"
+echo \
+"reldist count total fraction
+0.00 164 43408 0.004
+0.01 551 43408 0.013
+0.02 598 43408 0.014
+0.03 637 43408 0.015
+0.04 793 43408 0.018
+0.05 688 43408 0.016
+0.06 874 43408 0.020
+0.07 765 43408 0.018
+0.08 685 43408 0.016
+0.09 929 43408 0.021
+0.10 876 43408 0.020
+0.11 959 43408 0.022
+0.12 860 43408 0.020
+0.13 851 43408 0.020
+0.14 903 43408 0.021
+0.15 893 43408 0.021
+0.16 883 43408 0.020
+0.17 828 43408 0.019
+0.18 917 43408 0.021
+0.19 875 43408 0.020
+0.20 897 43408 0.021
+0.21 986 43408 0.023
+0.22 903 43408 0.021
+0.23 944 43408 0.022
+0.24 904 43408 0.021
+0.25 867 43408 0.020
+0.26 943 43408 0.022
+0.27 933 43408 0.021
+0.28 1132 43408 0.026
+0.29 881 43408 0.020
+0.30 851 43408 0.020
+0.31 963 43408 0.022
+0.32 950 43408 0.022
+0.33 965 43408 0.022
+0.34 907 43408 0.021
+0.35 884 43408 0.020
+0.36 965 43408 0.022
+0.37 944 43408 0.022
+0.38 911 43408 0.021
+0.39 939 43408 0.022
+0.40 921 43408 0.021
+0.41 950 43408 0.022
+0.42 935 43408 0.022
+0.43 919 43408 0.021
+0.44 915 43408 0.021
+0.45 934 43408 0.022
+0.46 843 43408 0.019
+0.47 850 43408 0.020
+0.48 1006 43408 0.023
+0.49 937 43408 0.022" > exp
+$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \
+ -b ../../data/aluY.chr1.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intervaks that are consistently closer to one another
+# than expected. The distances should be biased towards 0.=
+############################################################
+echo " reldist.t03...\c"
+echo \
+"reldist count total fraction
+0.00 20629 43422 0.475
+0.01 2629 43422 0.061
+0.02 1427 43422 0.033
+0.03 985 43422 0.023
+0.04 897 43422 0.021
+0.05 756 43422 0.017
+0.06 667 43422 0.015
+0.07 557 43422 0.013
+0.08 603 43422 0.014
+0.09 487 43422 0.011
+0.10 461 43422 0.011
+0.11 423 43422 0.010
+0.12 427 43422 0.010
+0.13 435 43422 0.010
+0.14 375 43422 0.009
+0.15 367 43422 0.008
+0.16 379 43422 0.009
+0.17 371 43422 0.009
+0.18 346 43422 0.008
+0.19 389 43422 0.009
+0.20 377 43422 0.009
+0.21 411 43422 0.009
+0.22 377 43422 0.009
+0.23 352 43422 0.008
+0.24 334 43422 0.008
+0.25 315 43422 0.007
+0.26 370 43422 0.009
+0.27 330 43422 0.008
+0.28 330 43422 0.008
+0.29 280 43422 0.006
+0.30 309 43422 0.007
+0.31 326 43422 0.008
+0.32 287 43422 0.007
+0.33 294 43422 0.007
+0.34 306 43422 0.007
+0.35 307 43422 0.007
+0.36 309 43422 0.007
+0.37 271 43422 0.006
+0.38 293 43422 0.007
+0.39 311 43422 0.007
+0.40 331 43422 0.008
+0.41 320 43422 0.007
+0.42 299 43422 0.007
+0.43 327 43422 0.008
+0.44 321 43422 0.007
+0.45 326 43422 0.008
+0.46 306 43422 0.007
+0.47 354 43422 0.008
+0.48 365 43422 0.008
+0.49 336 43422 0.008
+0.50 38 43422 0.001" > exp
+$BT reldist -a ../../data/refseq.chr1.exons.bed.gz \
+ -b ../../data/gerp.chr1.bed.gz > obs
+check obs exp
+rm obs exp
\ No newline at end of file
diff --git a/test/sample/human.hg19.genome b/test/sample/human.hg19.genome
new file mode 100644
index 0000000..d22ce2d
--- /dev/null
+++ b/test/sample/human.hg19.genome
@@ -0,0 +1,94 @@
+
+chr1 249250621
+chr10 135534747
+chr11 135006516
+chr11_gl000202_random 40103
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr17_ctg5_hap1 1680828
+chr17_gl000203_random 37498
+chr17_gl000204_random 81310
+chr17_gl000205_random 174588
+chr17_gl000206_random 41001
+chr18 78077248
+chr18_gl000207_random 4262
+chr19 59128983
+chr19_gl000208_random 92689
+chr19_gl000209_random 159169
+chr1_gl000191_random 106433
+chr1_gl000192_random 547496
+chr2 243199373
+chr20 63025520
+chr21 48129895
+chr21_gl000210_random 27682
+chr22 51304566
+chr3 198022430
+chr4 191154276
+chr4_ctg9_hap1 590426
+chr4_gl000193_random 189789
+chr4_gl000194_random 191469
+chr5 180915260
+chr6 171115067
+chr6_apd_hap1 4622290
+chr6_cox_hap2 4795371
+chr6_dbb_hap3 4610396
+chr6_mann_hap4 4683263
+chr6_mcf_hap5 4833398
+chr6_qbl_hap6 4611984
+chr6_ssto_hap7 4928567
+chr7 159138663
+chr7_gl000195_random 182896
+chr8 146364022
+chr8_gl000196_random 38914
+chr8_gl000197_random 37175
+chr9 141213431
+chr9_gl000198_random 90085
+chr9_gl000199_random 169874
+chr9_gl000200_random 187035
+chr9_gl000201_random 36148
+chrM 16571
+chrUn_gl000211 166566
+chrUn_gl000212 186858
+chrUn_gl000213 164239
+chrUn_gl000214 137718
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chrUn_gl000218 161147
+chrUn_gl000219 179198
+chrUn_gl000220 161802
+chrUn_gl000221 155397
+chrUn_gl000222 186861
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000225 211173
+chrUn_gl000226 15008
+chrUn_gl000227 128374
+chrUn_gl000228 129120
+chrUn_gl000229 19913
+chrUn_gl000230 43691
+chrUn_gl000231 27386
+chrUn_gl000232 40652
+chrUn_gl000233 45941
+chrUn_gl000234 40531
+chrUn_gl000235 34474
+chrUn_gl000236 41934
+chrUn_gl000237 45867
+chrUn_gl000238 39939
+chrUn_gl000239 33824
+chrUn_gl000240 41933
+chrUn_gl000241 42152
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000244 39929
+chrUn_gl000245 36651
+chrUn_gl000246 38154
+chrUn_gl000247 36422
+chrUn_gl000248 39786
+chrUn_gl000249 38502
+chrX 155270560
+chrY 59373566
diff --git a/test/sample/sample_help_withoutVersion.txt b/test/sample/sample_help_withoutVersion.txt
new file mode 100644
index 0000000..9d046ff
--- /dev/null
+++ b/test/sample/sample_help_withoutVersion.txt
@@ -0,0 +1,33 @@
+
+Tool: bedtools sample (aka sampleFile)
+Summary: Take sample of input file(s) using reservoir sampling algorithm.
+
+Usage: bedtools sample [OPTIONS] -i <bed/gff/vcf/bam>
+
+WARNING: The current sample algorithm will hold all requested sample records in memory prior to output.
+ The user must ensure that there is adequate memory for this.
+
+Options:
+ -n The number of records to generate.
+ - Default = 1,000,000.
+ - (INTEGER)
+
+ -seed Supply an integer seed for the shuffling.
+ - By default, the seed is chosen automatically.
+ - (INTEGER)
+
+ -ubam Write uncompressed BAM output. Default writes compressed BAM.
+
+ -bed When using BAM input (-abam), write output as BED. The default
+ is to write output in BAM when using -abam.
+
+ -s Require same strandedness. That is, only give records
+ that have the same strand. Use '-s forward' or '-s reverse'
+ for forward or reverse strand records, respectively.
+ - By default, records are reported without respect to strand.
+
+ -header Print the header from the input file prior to results.
+
+Notes:
+ TBD: Enter other usage notes here.
+
diff --git a/test/sample/test-sample.sh b/test/sample/test-sample.sh
new file mode 100644
index 0000000..5a65085
--- /dev/null
+++ b/test/sample/test-sample.sh
@@ -0,0 +1,124 @@
+###########################################################
+#
+# Unit tests for sampleFile program
+#
+############################################################
+
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+#
+# Create a 1,000 record BED6 file named "mainFile.bed".
+# Give it a one line header, to test the -header option.
+#
+###########################################################
+echo "#This is the mainFile from which samples will be taken." > mainFile.bed
+$BT random -l 1000 -n 1000 -g human.hg19.genome >> mainFile.bed
+
+
+
+###########################################################
+# Test that help is printed when no args are given
+############################################################
+echo " sample.t01...\c"
+$BT sample 2>&1 > /dev/null | grep -iv version > obs
+check obs sample_help_withoutVersion.txt
+rm obs
+
+
+###########################################################
+# Test that we throw an error for unrecognized arguments
+############################################################
+echo " sample.new.t02...\c"
+echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp
+$BT sample -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when no input file is given
+############################################################
+echo " sample.new.t03...\c"
+echo "***** ERROR: input file not specified. *****" > exp
+$BT sample -n 10 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -i without input file
+############################################################
+echo " sample.new.t04...\c"
+echo "***** ERROR: -i option given, but no input file specified. *****" > exp
+$BT sample -i 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error for -n given without
+# number of output records sepcified.
+############################################################
+echo " sample.new.t05...\c"
+echo "***** ERROR: -n option given, but no number of output records specified. *****" > exp
+$BT sample -n 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we throw an error when num output records
+# exceeds records in file.
+############################################################
+echo " sample.new.t06...\c"
+echo "***** ERROR: Input file has fewer records than the requested number of output records. *****" > exp
+$BT sample -i mainFile.bed 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we get the requested number of records
+############################################################
+echo " sample.new.t07...\c"
+echo "10" > exp
+$BT sample -i mainFile.bed -n 10 | wc -l > obs
+check obs exp
+#rm obs exp
+
+
+###########################################################
+# Test that the -seed option gives consistent results
+############################################################
+echo " sample.new.t08...\c"
+$BT sample -i mainFile.bed -n 50 -seed 4 > obs
+$BT sample -i mainFile.bed -n 50 -seed 4 > exp
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that -header option gives header
+############################################################
+echo " sample.new.t09...\c"
+echo "#This is the mainFile from which samples will be taken." > exp
+$BT sample -i mainFile.bed -n 10 -header | head -1 > obs
+check obs exp
+rm obs exp
+
+rm mainFile.bed
+
+
+
+
+
diff --git a/test/slop/test-slop.sh b/test/slop/test-slop.sh
index 51997f3..d11ce3a 100644
--- a/test/slop/test-slop.sh
+++ b/test/slop/test-slop.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
diff --git a/test/subtract/c.bed b/test/subtract/c.bed
new file mode 100644
index 0000000..63a66be
--- /dev/null
+++ b/test/subtract/c.bed
@@ -0,0 +1 @@
+chr1 0 10
diff --git a/test/subtract/d.bed b/test/subtract/d.bed
new file mode 100644
index 0000000..caceeca
--- /dev/null
+++ b/test/subtract/d.bed
@@ -0,0 +1,2 @@
+chr1 0 2
+chr1 4 6
diff --git a/test/subtract/test-subtract.sh b/test/subtract/test-subtract.sh
index 80281c0..8b71a98 100644
--- a/test/subtract/test-subtract.sh
+++ b/test/subtract/test-subtract.sh
@@ -1,4 +1,4 @@
-BT=../../bin/bedtools
+BT=${BT-../../bin/bedtools}
check()
{
@@ -111,3 +111,23 @@ echo \
$BT subtract -a a.bed -b b.bed -A -f 0.1 > obs
check obs exp
rm obs exp
+
+
+###########################################################
+# test -N with -f subtraction
+###########################################################
+echo " subtract.t9...\c"
+echo \
+"chr1 0 10" > exp
+$BT subtract -a c.bed -b d.bed -N -f 0.4 > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test -N with -f subtraction
+###########################################################
+echo " subtract.t10...\c"
+touch exp
+$BT subtract -a c.bed -b d.bed -N -f 0.39 > obs
+check obs exp
+rm obs exp
\ No newline at end of file
diff --git a/test/test.sh b/test/test.sh
index bf0e75b..a8eceba 100644
--- a/test/test.sh
+++ b/test/test.sh
@@ -1,50 +1,57 @@
echo " Performing general tests:"
-cd general; sh test-general.sh; cd ..
+cd general; bash test-general.sh; cd ..
echo " Testing bedtools bed12tobed6:"
-cd bed12tobed6; sh test-bed12tobed6.sh; cd ..
+cd bed12tobed6; bash test-bed12tobed6.sh; cd ..
echo " Testing bedtools bamtobed:"
-cd bamtobed; sh test-bamtobed.sh; cd ..
+cd bamtobed; bash test-bamtobed.sh; cd ..
echo " Testing bedtools closest:"
-cd closest; sh test-closest.sh; cd ..
+cd closest; bash test-closest.sh; cd ..
echo " Testing bedtools cluster:"
-cd cluster; sh test-cluster.sh; cd ..
+cd cluster; bash test-cluster.sh; cd ..
echo " Testing bedtools coverage:"
-cd coverage; sh test-coverage.sh; cd ..
+cd coverage; bash test-coverage.sh; cd ..
echo " Testing bedtools expand:"
-cd expand; sh test-expand.sh; cd ..
+cd expand; bash test-expand.sh; cd ..
echo " Testing bedtools flank:"
-cd flank; sh test-flank.sh; cd ..
+cd flank; bash test-flank.sh; cd ..
echo " Testing bedtools genomecov:"
-cd genomecov; sh test-genomecov.sh; cd ..
+cd genomecov; bash test-genomecov.sh; cd ..
echo " Testing bedtools getfasta:"
-cd getfasta; sh test-getfasta.sh; cd ..
+cd getfasta; bash test-getfasta.sh; cd ..
echo " Testing bedtools intersect:"
-cd intersect; sh test-intersect.sh; cd ..
+cd intersect; bash test-intersect.sh; bash new_test-intersect.sh; cd ..
echo " Testing bedtools jaccard:"
-cd jaccard; sh test-jaccard.sh; cd ..
+cd jaccard; bash test-jaccard.sh; cd ..
echo " Testing bedtools map:"
-cd map; sh test-map.sh; cd ..
+cd map; bash test-map.sh; cd ..
echo " Testing bedtools merge:"
-cd merge; sh test-merge.sh; cd ..
+cd merge; bash test-merge.sh; cd ..
echo " Testing bedtools multicov:"
-cd multicov; sh test-multicov.sh; cd ..
+cd multicov; bash test-multicov.sh; cd ..
+
+echo " Testing bedtools reldist:"
+cd reldist; bash test-reldist.sh; cd ..
echo " Testing bedtools slop:"
-cd slop; sh test-slop.sh; cd ..
+cd slop; bash test-slop.sh; cd ..
echo " Testing bedtools subtract:"
-cd subtract; sh test-subtract.sh; cd ..
+cd subtract; bash test-subtract.sh; cd ..
+
+echo " Testing bedtools sample:"
+cd sample; bash test-sample.sh; cd ..
+
--
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