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liulab-dfci · Aug 14, 2019 · a9d1456 · a9d1456
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diff --git a/pkg/.DS_Store b/pkg/.DS_Store
diff --git a/pkg/Dr.seq.1.2.0/bin/Drseq.pyc b/pkg/Dr.seq.1.2.0/bin/Drseq.pyc
diff --git a/pkg/Dr.seq.1.2.0/lib/Utility.pyc b/pkg/Dr.seq.1.2.0/lib/Utility.pyc
diff --git a/pkg/Rabit/.project b/pkg/Rabit/.project
diff --git a/pkg/Dr.seq.1.2.0/LICENSE → refpkg/Dr.seq.1.2.0/LICENSE b/pkg/Dr.seq.1.2.0/LICENSE → refpkg/Dr.seq.1.2.0/LICENSE
diff --git a/pkg/Dr.seq.1.2.0/README.md → refpkg/Dr.seq.1.2.0/README.md b/pkg/Dr.seq.1.2.0/README.md → refpkg/Dr.seq.1.2.0/README.md
diff --git a/pkg/Dr.seq.1.2.0/README/FAQ.pdf → refpkg/Dr.seq.1.2.0/README/FAQ.pdf b/pkg/Dr.seq.1.2.0/README/FAQ.pdf → refpkg/Dr.seq.1.2.0/README/FAQ.pdf
diff --git a/pkg/Dr.seq.1.2.0/README/Manual.pdf → refpkg/Dr.seq.1.2.0/README/Manual.pdf b/pkg/Dr.seq.1.2.0/README/Manual.pdf → refpkg/Dr.seq.1.2.0/README/Manual.pdf
diff --git a/pkg/Dr.seq.1.2.0/README/Quick_start.pdf → refpkg/Dr.seq.1.2.0/README/Quick_start.pdf b/pkg/Dr.seq.1.2.0/README/Quick_start.pdf → refpkg/Dr.seq.1.2.0/README/Quick_start.pdf
diff --git a/....seq.1.2.0/README/Summary_report_demo.pdf → ....seq.1.2.0/README/Summary_report_demo.pdf b/....seq.1.2.0/README/Summary_report_demo.pdf → ....seq.1.2.0/README/Summary_report_demo.pdf
diff --git a/pkg/Dr.seq.1.2.0/bin/Dropseq_MAESTRO.conf → refpkg/Dr.seq.1.2.0/bin/Dropseq_MAESTRO.conf b/pkg/Dr.seq.1.2.0/bin/Dropseq_MAESTRO.conf → refpkg/Dr.seq.1.2.0/bin/Dropseq_MAESTRO.conf
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diff --git a/pkg/Dr.seq.1.2.0/bin/Drseq.py → refpkg/Dr.seq.1.2.0/bin/Drseq.py b/pkg/Dr.seq.1.2.0/bin/Drseq.py → refpkg/Dr.seq.1.2.0/bin/Drseq.py
diff --git a/....seq.1.2.0/lib/Config/Drseq_template.conf → ....seq.1.2.0/lib/Config/Drseq_template.conf b/....seq.1.2.0/lib/Config/Drseq_template.conf → ....seq.1.2.0/lib/Config/Drseq_template.conf
diff --git a/pkg/Dr.seq.1.2.0/lib/Rscript/analysis.r → refpkg/Dr.seq.1.2.0/lib/Rscript/analysis.r b/pkg/Dr.seq.1.2.0/lib/Rscript/analysis.r → refpkg/Dr.seq.1.2.0/lib/Rscript/analysis.r
diff --git a/pkg/Dr.seq.1.2.0/lib/Rscript/individual_qc.r → .../Dr.seq.1.2.0/lib/Rscript/individual_qc.r b/pkg/Dr.seq.1.2.0/lib/Rscript/individual_qc.r → .../Dr.seq.1.2.0/lib/Rscript/individual_qc.r
diff --git a/pkg/Dr.seq.1.2.0/lib/Rscript/post_analysis.r → .../Dr.seq.1.2.0/lib/Rscript/post_analysis.r b/pkg/Dr.seq.1.2.0/lib/Rscript/post_analysis.r → .../Dr.seq.1.2.0/lib/Rscript/post_analysis.r
diff --git a/pkg/Dr.seq.1.2.0/lib/Rscript/readsbulkQC.r → ...kg/Dr.seq.1.2.0/lib/Rscript/readsbulkQC.r b/pkg/Dr.seq.1.2.0/lib/Rscript/readsbulkQC.r → ...kg/Dr.seq.1.2.0/lib/Rscript/readsbulkQC.r
diff --git a/pkg/Dr.seq.1.2.0/lib/Utility.py → refpkg/Dr.seq.1.2.0/lib/Utility.py b/pkg/Dr.seq.1.2.0/lib/Utility.py → refpkg/Dr.seq.1.2.0/lib/Utility.py
diff --git a/pkg/Dr.seq.1.2.0/lib/__init__.py → refpkg/Dr.seq.1.2.0/lib/__init__.py b/pkg/Dr.seq.1.2.0/lib/__init__.py → refpkg/Dr.seq.1.2.0/lib/__init__.py
diff --git a/pkg/Dr.seq.1.2.0/lib/parse_config.py → refpkg/Dr.seq.1.2.0/lib/parse_config.py b/pkg/Dr.seq.1.2.0/lib/parse_config.py → refpkg/Dr.seq.1.2.0/lib/parse_config.py
diff --git a/pkg/Dr.seq.1.2.0/lib/step0_integrate_data.py → .../Dr.seq.1.2.0/lib/step0_integrate_data.py b/pkg/Dr.seq.1.2.0/lib/step0_integrate_data.py → .../Dr.seq.1.2.0/lib/step0_integrate_data.py
diff --git a/...Dr.seq.1.2.0/lib/step1_generate_matrix.py → ...Dr.seq.1.2.0/lib/step1_generate_matrix.py b/...Dr.seq.1.2.0/lib/step1_generate_matrix.py → ...Dr.seq.1.2.0/lib/step1_generate_matrix.py
diff --git a/pkg/Dr.seq.1.2.0/lib/step3_QC.py → refpkg/Dr.seq.1.2.0/lib/step3_QC.py b/pkg/Dr.seq.1.2.0/lib/step3_QC.py → refpkg/Dr.seq.1.2.0/lib/step3_QC.py
diff --git a/pkg/Dr.seq.1.2.0/lib/step4_analysis.py → refpkg/Dr.seq.1.2.0/lib/step4_analysis.py b/pkg/Dr.seq.1.2.0/lib/step4_analysis.py → refpkg/Dr.seq.1.2.0/lib/step4_analysis.py
diff --git a/pkg/Dr.seq.1.2.0/lib/step5_summary.py → refpkg/Dr.seq.1.2.0/lib/step5_summary.py b/pkg/Dr.seq.1.2.0/lib/step5_summary.py → refpkg/Dr.seq.1.2.0/lib/step5_summary.py
diff --git a/pkg/Dr.seq.1.2.0/refpackage/bedtools/LICENSE → .../Dr.seq.1.2.0/refpackage/bedtools/LICENSE b/pkg/Dr.seq.1.2.0/refpackage/bedtools/LICENSE → .../Dr.seq.1.2.0/refpackage/bedtools/LICENSE
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diff --git a/...ackage/bedtools/genomes/human.hg18.genome → ...ackage/bedtools/genomes/human.hg18.genome b/...ackage/bedtools/genomes/human.hg18.genome → ...ackage/bedtools/genomes/human.hg18.genome
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diff --git a/...package/bedtools/genomes/mouse.mm8.genome → ...package/bedtools/genomes/mouse.mm8.genome b/...package/bedtools/genomes/mouse.mm8.genome → ...package/bedtools/genomes/mouse.mm8.genome
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diff --git a/...ckage/bedtools/scripts/makeBashScripts.py → ...ckage/bedtools/scripts/makeBashScripts.py b/...ckage/bedtools/scripts/makeBashScripts.py → ...ckage/bedtools/scripts/makeBashScripts.py
diff --git a/...package/bedtools/src/annotateBed/Makefile → ...package/bedtools/src/annotateBed/Makefile b/...package/bedtools/src/annotateBed/Makefile → ...package/bedtools/src/annotateBed/Makefile
diff --git a/.../bedtools/src/annotateBed/annotateBed.cpp → .../bedtools/src/annotateBed/annotateBed.cpp b/.../bedtools/src/annotateBed/annotateBed.cpp → .../bedtools/src/annotateBed/annotateBed.cpp
diff --git a/...ge/bedtools/src/annotateBed/annotateBed.h → ...ge/bedtools/src/annotateBed/annotateBed.h b/...ge/bedtools/src/annotateBed/annotateBed.h → ...ge/bedtools/src/annotateBed/annotateBed.h
diff --git a/...bedtools/src/annotateBed/annotateMain.cpp → ...bedtools/src/annotateBed/annotateMain.cpp b/...bedtools/src/annotateBed/annotateMain.cpp → ...bedtools/src/annotateBed/annotateMain.cpp
diff --git a/...refpackage/bedtools/src/bamToBed/Makefile → ...refpackage/bedtools/src/bamToBed/Makefile b/...refpackage/bedtools/src/bamToBed/Makefile → ...refpackage/bedtools/src/bamToBed/Makefile
diff --git a/...ackage/bedtools/src/bamToBed/bamToBed.cpp → ...ackage/bedtools/src/bamToBed/bamToBed.cpp b/...ackage/bedtools/src/bamToBed/bamToBed.cpp → ...ackage/bedtools/src/bamToBed/bamToBed.cpp
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diff --git a/...edtools/src/bamToFastq/bamToFastqMain.cpp → ...edtools/src/bamToFastq/bamToFastqMain.cpp b/...edtools/src/bamToFastq/bamToFastqMain.cpp → ...edtools/src/bamToFastq/bamToFastqMain.cpp
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diff --git a/...package/bedtools/src/bedpeToBam/notes.txt → ...package/bedtools/src/bedpeToBam/notes.txt b/...package/bedtools/src/bedpeToBam/notes.txt → ...package/bedtools/src/bedpeToBam/notes.txt
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diff --git a/...e/bedtools/src/closestBed/closestMain.cpp → ...e/bedtools/src/closestBed/closestMain.cpp b/...e/bedtools/src/closestBed/closestMain.cpp → ...e/bedtools/src/closestBed/closestMain.cpp
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diff --git a/...e/bedtools/src/clusterBed/clusterMain.cpp → ...e/bedtools/src/clusterBed/clusterMain.cpp b/...e/bedtools/src/clusterBed/clusterMain.cpp → ...e/bedtools/src/clusterBed/clusterMain.cpp
diff --git a/...ckage/bedtools/src/complementBed/Makefile → ...ckage/bedtools/src/complementBed/Makefile b/...ckage/bedtools/src/complementBed/Makefile → ...ckage/bedtools/src/complementBed/Makefile
diff --git a/...tools/src/complementBed/complementBed.cpp → ...tools/src/complementBed/complementBed.cpp b/...tools/src/complementBed/complementBed.cpp → ...tools/src/complementBed/complementBed.cpp
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diff --git a/...ools/src/complementBed/complementMain.cpp → ...ools/src/complementBed/complementMain.cpp b/...ools/src/complementBed/complementMain.cpp → ...ools/src/complementBed/complementMain.cpp
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diff --git a/...e/bedtools/src/genomeCoverageBed/Makefile → ...e/bedtools/src/genomeCoverageBed/Makefile b/...e/bedtools/src/genomeCoverageBed/Makefile → ...e/bedtools/src/genomeCoverageBed/Makefile
diff --git a/...c/genomeCoverageBed/genomeCoverageBed.cpp → ...c/genomeCoverageBed/genomeCoverageBed.cpp b/...c/genomeCoverageBed/genomeCoverageBed.cpp → ...c/genomeCoverageBed/genomeCoverageBed.cpp
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diff --git a/.../genomeCoverageBed/genomeCoverageMain.cpp → .../genomeCoverageBed/genomeCoverageMain.cpp b/.../genomeCoverageBed/genomeCoverageMain.cpp → .../genomeCoverageBed/genomeCoverageMain.cpp
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diff --git a/...dtools/src/intersectBed/intersectMain.cpp → ...dtools/src/intersectBed/intersectMain.cpp b/...dtools/src/intersectBed/intersectMain.cpp → ...dtools/src/intersectBed/intersectMain.cpp
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diff --git a/...ckage/bedtools/src/linksBed/linksMain.cpp → ...ckage/bedtools/src/linksBed/linksMain.cpp b/...ckage/bedtools/src/linksBed/linksMain.cpp → ...ckage/bedtools/src/linksBed/linksMain.cpp
diff --git a/...0/refpackage/bedtools/src/mapBed/Makefile → ...0/refpackage/bedtools/src/mapBed/Makefile b/...0/refpackage/bedtools/src/mapBed/Makefile → ...0/refpackage/bedtools/src/mapBed/Makefile
diff --git a/...refpackage/bedtools/src/mapBed/mapBed.cpp → ...refpackage/bedtools/src/mapBed/mapBed.cpp b/...refpackage/bedtools/src/mapBed/mapBed.cpp → ...refpackage/bedtools/src/mapBed/mapBed.cpp
diff --git a/...0/refpackage/bedtools/src/mapBed/mapBed.h → ...0/refpackage/bedtools/src/mapBed/mapBed.h b/...0/refpackage/bedtools/src/mapBed/mapBed.h → ...0/refpackage/bedtools/src/mapBed/mapBed.h
diff --git a/...efpackage/bedtools/src/mapBed/mapMain.cpp → ...efpackage/bedtools/src/mapBed/mapMain.cpp b/...efpackage/bedtools/src/mapBed/mapMain.cpp → ...efpackage/bedtools/src/mapBed/mapMain.cpp
diff --git a/...ge/bedtools/src/maskFastaFromBed/Makefile → ...ge/bedtools/src/maskFastaFromBed/Makefile b/...ge/bedtools/src/maskFastaFromBed/Makefile → ...ge/bedtools/src/maskFastaFromBed/Makefile
diff --git a/...src/maskFastaFromBed/maskFastaFromBed.cpp → ...src/maskFastaFromBed/maskFastaFromBed.cpp b/...src/maskFastaFromBed/maskFastaFromBed.cpp → ...src/maskFastaFromBed/maskFastaFromBed.cpp
diff --git a/...s/src/maskFastaFromBed/maskFastaFromBed.h → ...s/src/maskFastaFromBed/maskFastaFromBed.h b/...s/src/maskFastaFromBed/maskFastaFromBed.h → ...s/src/maskFastaFromBed/maskFastaFromBed.h
diff --git a/...maskFastaFromBed/maskFastaFromBedMain.cpp → ...maskFastaFromBed/maskFastaFromBedMain.cpp b/...maskFastaFromBed/maskFastaFromBedMain.cpp → ...maskFastaFromBed/maskFastaFromBedMain.cpp
diff --git a/...refpackage/bedtools/src/mergeBed/Makefile → ...refpackage/bedtools/src/mergeBed/Makefile b/...refpackage/bedtools/src/mergeBed/Makefile → ...refpackage/bedtools/src/mergeBed/Makefile
diff --git a/...ackage/bedtools/src/mergeBed/mergeBed.cpp → ...ackage/bedtools/src/mergeBed/mergeBed.cpp b/...ackage/bedtools/src/mergeBed/mergeBed.cpp → ...ackage/bedtools/src/mergeBed/mergeBed.cpp
diff --git a/...fpackage/bedtools/src/mergeBed/mergeBed.h → ...fpackage/bedtools/src/mergeBed/mergeBed.h b/...fpackage/bedtools/src/mergeBed/mergeBed.h → ...fpackage/bedtools/src/mergeBed/mergeBed.h
diff --git a/...ckage/bedtools/src/mergeBed/mergeMain.cpp → ...ckage/bedtools/src/mergeBed/mergeMain.cpp b/...ckage/bedtools/src/mergeBed/mergeMain.cpp → ...ckage/bedtools/src/mergeBed/mergeMain.cpp
diff --git a/...package/bedtools/src/multiBamCov/Makefile → ...package/bedtools/src/multiBamCov/Makefile b/...package/bedtools/src/multiBamCov/Makefile → ...package/bedtools/src/multiBamCov/Makefile
diff --git a/.../bedtools/src/multiBamCov/multiBamCov.cpp → .../bedtools/src/multiBamCov/multiBamCov.cpp b/.../bedtools/src/multiBamCov/multiBamCov.cpp → .../bedtools/src/multiBamCov/multiBamCov.cpp
diff --git a/...ge/bedtools/src/multiBamCov/multiBamCov.h → ...ge/bedtools/src/multiBamCov/multiBamCov.h b/...ge/bedtools/src/multiBamCov/multiBamCov.h → ...ge/bedtools/src/multiBamCov/multiBamCov.h
diff --git a/...tools/src/multiBamCov/multiBamCovMain.cpp → ...tools/src/multiBamCov/multiBamCovMain.cpp b/...tools/src/multiBamCov/multiBamCovMain.cpp → ...tools/src/multiBamCov/multiBamCovMain.cpp
diff --git a/...e/bedtools/src/multiIntersectBed/Makefile → ...e/bedtools/src/multiIntersectBed/Makefile b/...e/bedtools/src/multiIntersectBed/Makefile → ...e/bedtools/src/multiIntersectBed/Makefile
diff --git a/...c/multiIntersectBed/multiIntersectBed.cpp → ...c/multiIntersectBed/multiIntersectBed.cpp b/...c/multiIntersectBed/multiIntersectBed.cpp → ...c/multiIntersectBed/multiIntersectBed.cpp
diff --git a/...src/multiIntersectBed/multiIntersectBed.h → ...src/multiIntersectBed/multiIntersectBed.h b/...src/multiIntersectBed/multiIntersectBed.h → ...src/multiIntersectBed/multiIntersectBed.h
diff --git a/...ltiIntersectBed/multiIntersectBedMain.cpp → ...ltiIntersectBed/multiIntersectBedMain.cpp b/...ltiIntersectBed/multiIntersectBedMain.cpp → ...ltiIntersectBed/multiIntersectBedMain.cpp
diff --git a/...ge/bedtools/src/nucBed/LargeFileSupport.h → ...ge/bedtools/src/nucBed/LargeFileSupport.h b/...ge/bedtools/src/nucBed/LargeFileSupport.h → ...ge/bedtools/src/nucBed/LargeFileSupport.h
diff --git a/...0/refpackage/bedtools/src/nucBed/Makefile → ...0/refpackage/bedtools/src/nucBed/Makefile b/...0/refpackage/bedtools/src/nucBed/Makefile → ...0/refpackage/bedtools/src/nucBed/Makefile
diff --git a/...refpackage/bedtools/src/nucBed/nucBed.cpp → ...refpackage/bedtools/src/nucBed/nucBed.cpp b/...refpackage/bedtools/src/nucBed/nucBed.cpp → ...refpackage/bedtools/src/nucBed/nucBed.cpp
diff --git a/...0/refpackage/bedtools/src/nucBed/nucBed.h → ...0/refpackage/bedtools/src/nucBed/nucBed.h b/...0/refpackage/bedtools/src/nucBed/nucBed.h → ...0/refpackage/bedtools/src/nucBed/nucBed.h
diff --git a/...ackage/bedtools/src/nucBed/nucBedMain.cpp → ...ackage/bedtools/src/nucBed/nucBedMain.cpp b/...ackage/bedtools/src/nucBed/nucBedMain.cpp → ...ackage/bedtools/src/nucBed/nucBedMain.cpp
diff --git a/...efpackage/bedtools/src/pairToBed/Makefile → ...efpackage/bedtools/src/pairToBed/Makefile b/...efpackage/bedtools/src/pairToBed/Makefile → ...efpackage/bedtools/src/pairToBed/Makefile
diff --git a/...kage/bedtools/src/pairToBed/pairToBed.cpp → ...kage/bedtools/src/pairToBed/pairToBed.cpp b/...kage/bedtools/src/pairToBed/pairToBed.cpp → ...kage/bedtools/src/pairToBed/pairToBed.cpp
diff --git a/...ackage/bedtools/src/pairToBed/pairToBed.h → ...ackage/bedtools/src/pairToBed/pairToBed.h b/...ackage/bedtools/src/pairToBed/pairToBed.h → ...ackage/bedtools/src/pairToBed/pairToBed.h
diff --git a/.../bedtools/src/pairToBed/pairToBedMain.cpp → .../bedtools/src/pairToBed/pairToBedMain.cpp b/.../bedtools/src/pairToBed/pairToBedMain.cpp → .../bedtools/src/pairToBed/pairToBedMain.cpp
diff --git a/...fpackage/bedtools/src/pairToPair/Makefile → ...fpackage/bedtools/src/pairToPair/Makefile b/...fpackage/bedtools/src/pairToPair/Makefile → ...fpackage/bedtools/src/pairToPair/Makefile
diff --git a/...ge/bedtools/src/pairToPair/pairToPair.cpp → ...ge/bedtools/src/pairToPair/pairToPair.cpp b/...ge/bedtools/src/pairToPair/pairToPair.cpp → ...ge/bedtools/src/pairToPair/pairToPair.cpp
diff --git a/...kage/bedtools/src/pairToPair/pairToPair.h → ...kage/bedtools/src/pairToPair/pairToPair.h b/...kage/bedtools/src/pairToPair/pairToPair.h → ...kage/bedtools/src/pairToPair/pairToPair.h
diff --git a/...edtools/src/pairToPair/pairToPairMain.cpp → ...edtools/src/pairToPair/pairToPairMain.cpp b/...edtools/src/pairToPair/pairToPairMain.cpp → ...edtools/src/pairToPair/pairToPairMain.cpp
diff --git a/...efpackage/bedtools/src/randomBed/Makefile → ...efpackage/bedtools/src/randomBed/Makefile b/...efpackage/bedtools/src/randomBed/Makefile → ...efpackage/bedtools/src/randomBed/Makefile
diff --git a/...kage/bedtools/src/randomBed/randomBed.cpp → ...kage/bedtools/src/randomBed/randomBed.cpp b/...kage/bedtools/src/randomBed/randomBed.cpp → ...kage/bedtools/src/randomBed/randomBed.cpp
diff --git a/...ackage/bedtools/src/randomBed/randomBed.h → ...ackage/bedtools/src/randomBed/randomBed.h b/...ackage/bedtools/src/randomBed/randomBed.h → ...ackage/bedtools/src/randomBed/randomBed.h
diff --git a/.../bedtools/src/randomBed/randomBedMain.cpp → .../bedtools/src/randomBed/randomBedMain.cpp b/.../bedtools/src/randomBed/randomBedMain.cpp → .../bedtools/src/randomBed/randomBedMain.cpp
diff --git a/.../refpackage/bedtools/src/reldist/Makefile → .../refpackage/bedtools/src/reldist/Makefile b/.../refpackage/bedtools/src/reldist/Makefile → .../refpackage/bedtools/src/reldist/Makefile
diff --git a/...fpackage/bedtools/src/reldist/reldist.cpp → ...fpackage/bedtools/src/reldist/reldist.cpp b/...fpackage/bedtools/src/reldist/reldist.cpp → ...fpackage/bedtools/src/reldist/reldist.cpp
diff --git a/...refpackage/bedtools/src/reldist/reldist.h → ...refpackage/bedtools/src/reldist/reldist.h b/...refpackage/bedtools/src/reldist/reldist.h → ...refpackage/bedtools/src/reldist/reldist.h
diff --git a/...kage/bedtools/src/reldist/reldistMain.cpp → ...kage/bedtools/src/reldist/reldistMain.cpp b/...kage/bedtools/src/reldist/reldistMain.cpp → ...kage/bedtools/src/reldist/reldistMain.cpp
diff --git a/...fpackage/bedtools/src/shuffleBed/Makefile → ...fpackage/bedtools/src/shuffleBed/Makefile b/...fpackage/bedtools/src/shuffleBed/Makefile → ...fpackage/bedtools/src/shuffleBed/Makefile
diff --git a/...ge/bedtools/src/shuffleBed/shuffleBed.cpp → ...ge/bedtools/src/shuffleBed/shuffleBed.cpp b/...ge/bedtools/src/shuffleBed/shuffleBed.cpp → ...ge/bedtools/src/shuffleBed/shuffleBed.cpp
diff --git a/...kage/bedtools/src/shuffleBed/shuffleBed.h → ...kage/bedtools/src/shuffleBed/shuffleBed.h b/...kage/bedtools/src/shuffleBed/shuffleBed.h → ...kage/bedtools/src/shuffleBed/shuffleBed.h
diff --git a/...edtools/src/shuffleBed/shuffleBedMain.cpp → ...edtools/src/shuffleBed/shuffleBedMain.cpp b/...edtools/src/shuffleBed/shuffleBedMain.cpp → ...edtools/src/shuffleBed/shuffleBedMain.cpp
diff --git a/.../refpackage/bedtools/src/slopBed/Makefile → .../refpackage/bedtools/src/slopBed/Makefile b/.../refpackage/bedtools/src/slopBed/Makefile → .../refpackage/bedtools/src/slopBed/Makefile
diff --git a/...fpackage/bedtools/src/slopBed/slopBed.cpp → ...fpackage/bedtools/src/slopBed/slopBed.cpp b/...fpackage/bedtools/src/slopBed/slopBed.cpp → ...fpackage/bedtools/src/slopBed/slopBed.cpp
diff --git a/...refpackage/bedtools/src/slopBed/slopBed.h → ...refpackage/bedtools/src/slopBed/slopBed.h b/...refpackage/bedtools/src/slopBed/slopBed.h → ...refpackage/bedtools/src/slopBed/slopBed.h
diff --git a/...kage/bedtools/src/slopBed/slopBedMain.cpp → ...kage/bedtools/src/slopBed/slopBedMain.cpp b/...kage/bedtools/src/slopBed/slopBedMain.cpp → ...kage/bedtools/src/slopBed/slopBedMain.cpp
diff --git a/.../refpackage/bedtools/src/sortBed/Makefile → .../refpackage/bedtools/src/sortBed/Makefile b/.../refpackage/bedtools/src/sortBed/Makefile → .../refpackage/bedtools/src/sortBed/Makefile
diff --git a/...fpackage/bedtools/src/sortBed/sortBed.cpp → ...fpackage/bedtools/src/sortBed/sortBed.cpp b/...fpackage/bedtools/src/sortBed/sortBed.cpp → ...fpackage/bedtools/src/sortBed/sortBed.cpp
diff --git a/...refpackage/bedtools/src/sortBed/sortBed.h → ...refpackage/bedtools/src/sortBed/sortBed.h b/...refpackage/bedtools/src/sortBed/sortBed.h → ...refpackage/bedtools/src/sortBed/sortBed.h
diff --git a/...package/bedtools/src/sortBed/sortMain.cpp → ...package/bedtools/src/sortBed/sortMain.cpp b/...package/bedtools/src/sortBed/sortMain.cpp → ...package/bedtools/src/sortBed/sortMain.cpp
diff --git a/...package/bedtools/src/subtractBed/Makefile → ...package/bedtools/src/subtractBed/Makefile b/...package/bedtools/src/subtractBed/Makefile → ...package/bedtools/src/subtractBed/Makefile
diff --git a/.../bedtools/src/subtractBed/subtractBed.cpp → .../bedtools/src/subtractBed/subtractBed.cpp b/.../bedtools/src/subtractBed/subtractBed.cpp → .../bedtools/src/subtractBed/subtractBed.cpp
diff --git a/...ge/bedtools/src/subtractBed/subtractBed.h → ...ge/bedtools/src/subtractBed/subtractBed.h b/...ge/bedtools/src/subtractBed/subtractBed.h → ...ge/bedtools/src/subtractBed/subtractBed.h
diff --git a/...bedtools/src/subtractBed/subtractMain.cpp → ...bedtools/src/subtractBed/subtractMain.cpp b/...bedtools/src/subtractBed/subtractMain.cpp → ...bedtools/src/subtractBed/subtractMain.cpp
diff --git a/...0/refpackage/bedtools/src/tagBam/Makefile → ...0/refpackage/bedtools/src/tagBam/Makefile b/...0/refpackage/bedtools/src/tagBam/Makefile → ...0/refpackage/bedtools/src/tagBam/Makefile
diff --git a/...refpackage/bedtools/src/tagBam/tagBam.cpp → ...refpackage/bedtools/src/tagBam/tagBam.cpp b/...refpackage/bedtools/src/tagBam/tagBam.cpp → ...refpackage/bedtools/src/tagBam/tagBam.cpp
diff --git a/...0/refpackage/bedtools/src/tagBam/tagBam.h → ...0/refpackage/bedtools/src/tagBam/tagBam.h b/...0/refpackage/bedtools/src/tagBam/tagBam.h → ...0/refpackage/bedtools/src/tagBam/tagBam.h
diff --git a/...ackage/bedtools/src/tagBam/tagBamMain.cpp → ...ackage/bedtools/src/tagBam/tagBamMain.cpp b/...ackage/bedtools/src/tagBam/tagBamMain.cpp → ...ackage/bedtools/src/tagBam/tagBamMain.cpp
diff --git a/...kage/bedtools/src/unionBedGraphs/Makefile → ...kage/bedtools/src/unionBedGraphs/Makefile b/...kage/bedtools/src/unionBedGraphs/Makefile → ...kage/bedtools/src/unionBedGraphs/Makefile
diff --git a/...ols/src/unionBedGraphs/unionBedGraphs.cpp → ...ols/src/unionBedGraphs/unionBedGraphs.cpp b/...ols/src/unionBedGraphs/unionBedGraphs.cpp → ...ols/src/unionBedGraphs/unionBedGraphs.cpp
diff --git a/...tools/src/unionBedGraphs/unionBedGraphs.h → ...tools/src/unionBedGraphs/unionBedGraphs.h b/...tools/src/unionBedGraphs/unionBedGraphs.h → ...tools/src/unionBedGraphs/unionBedGraphs.h
diff --git a/...src/unionBedGraphs/unionBedGraphsMain.cpp → ...src/unionBedGraphs/unionBedGraphsMain.cpp b/...src/unionBedGraphs/unionBedGraphsMain.cpp → ...src/unionBedGraphs/unionBedGraphsMain.cpp
diff --git a/...utils/BamTools-Ancillary/BamAncillary.cpp → ...utils/BamTools-Ancillary/BamAncillary.cpp b/...utils/BamTools-Ancillary/BamAncillary.cpp → ...utils/BamTools-Ancillary/BamAncillary.cpp
diff --git a/...c/utils/BamTools-Ancillary/BamAncillary.h → ...c/utils/BamTools-Ancillary/BamAncillary.h b/...c/utils/BamTools-Ancillary/BamAncillary.h → ...c/utils/BamTools-Ancillary/BamAncillary.h
diff --git a/...ols/src/utils/BamTools-Ancillary/Makefile → ...ols/src/utils/BamTools-Ancillary/Makefile b/...ols/src/utils/BamTools-Ancillary/Makefile → ...ols/src/utils/BamTools-Ancillary/Makefile
diff --git a/...ckage/bedtools/src/utils/BamTools/LICENSE → ...ckage/bedtools/src/utils/BamTools/LICENSE b/...ckage/bedtools/src/utils/BamTools/LICENSE → ...ckage/bedtools/src/utils/BamTools/LICENSE
diff --git a/...kage/bedtools/src/utils/BamTools/Makefile → ...kage/bedtools/src/utils/BamTools/Makefile b/...kage/bedtools/src/utils/BamTools/Makefile → ...kage/bedtools/src/utils/BamTools/Makefile
diff --git a/...rc/utils/BamTools/src/api/BamAlgorithms.h → ...rc/utils/BamTools/src/api/BamAlgorithms.h b/...rc/utils/BamTools/src/api/BamAlgorithms.h → ...rc/utils/BamTools/src/api/BamAlgorithms.h
diff --git a/...c/utils/BamTools/src/api/BamAlignment.cpp → ...c/utils/BamTools/src/api/BamAlignment.cpp b/...c/utils/BamTools/src/api/BamAlignment.cpp → ...c/utils/BamTools/src/api/BamAlignment.cpp
diff --git a/...src/utils/BamTools/src/api/BamAlignment.h → ...src/utils/BamTools/src/api/BamAlignment.h b/...src/utils/BamTools/src/api/BamAlignment.h → ...src/utils/BamTools/src/api/BamAlignment.h
diff --git a/...tools/src/utils/BamTools/src/api/BamAux.h → ...tools/src/utils/BamTools/src/api/BamAux.h b/...tools/src/utils/BamTools/src/api/BamAux.h → ...tools/src/utils/BamTools/src/api/BamAux.h
diff --git a/...src/utils/BamTools/src/api/BamConstants.h → ...src/utils/BamTools/src/api/BamConstants.h b/...src/utils/BamTools/src/api/BamConstants.h → ...src/utils/BamTools/src/api/BamConstants.h
diff --git a/...ols/src/utils/BamTools/src/api/BamIndex.h → ...ols/src/utils/BamTools/src/api/BamIndex.h b/...ols/src/utils/BamTools/src/api/BamIndex.h → ...ols/src/utils/BamTools/src/api/BamIndex.h
diff --git a/...utils/BamTools/src/api/BamMultiReader.cpp → ...utils/BamTools/src/api/BamMultiReader.cpp b/...utils/BamTools/src/api/BamMultiReader.cpp → ...utils/BamTools/src/api/BamMultiReader.cpp
diff --git a/...c/utils/BamTools/src/api/BamMultiReader.h → ...c/utils/BamTools/src/api/BamMultiReader.h b/...c/utils/BamTools/src/api/BamMultiReader.h → ...c/utils/BamTools/src/api/BamMultiReader.h
diff --git a/.../src/utils/BamTools/src/api/BamReader.cpp → .../src/utils/BamTools/src/api/BamReader.cpp b/.../src/utils/BamTools/src/api/BamReader.cpp → .../src/utils/BamTools/src/api/BamReader.cpp
diff --git a/...ls/src/utils/BamTools/src/api/BamReader.h → ...ls/src/utils/BamTools/src/api/BamReader.h b/...ls/src/utils/BamTools/src/api/BamReader.h → ...ls/src/utils/BamTools/src/api/BamReader.h
diff --git a/.../src/utils/BamTools/src/api/BamWriter.cpp → .../src/utils/BamTools/src/api/BamWriter.cpp b/.../src/utils/BamTools/src/api/BamWriter.cpp → .../src/utils/BamTools/src/api/BamWriter.cpp
diff --git a/...ls/src/utils/BamTools/src/api/BamWriter.h → ...ls/src/utils/BamTools/src/api/BamWriter.h b/...ls/src/utils/BamTools/src/api/BamWriter.h → ...ls/src/utils/BamTools/src/api/BamWriter.h
diff --git a/...src/utils/BamTools/src/api/IBamIODevice.h → ...src/utils/BamTools/src/api/IBamIODevice.h b/...src/utils/BamTools/src/api/IBamIODevice.h → ...src/utils/BamTools/src/api/IBamIODevice.h
diff --git a/...src/utils/BamTools/src/api/SamConstants.h → ...src/utils/BamTools/src/api/SamConstants.h b/...src/utils/BamTools/src/api/SamConstants.h → ...src/utils/BamTools/src/api/SamConstants.h
diff --git a/.../src/utils/BamTools/src/api/SamHeader.cpp → .../src/utils/BamTools/src/api/SamHeader.cpp b/.../src/utils/BamTools/src/api/SamHeader.cpp → .../src/utils/BamTools/src/api/SamHeader.cpp
diff --git a/...ls/src/utils/BamTools/src/api/SamHeader.h → ...ls/src/utils/BamTools/src/api/SamHeader.h b/...ls/src/utils/BamTools/src/api/SamHeader.h → ...ls/src/utils/BamTools/src/api/SamHeader.h
diff --git a/...src/utils/BamTools/src/api/SamProgram.cpp → ...src/utils/BamTools/src/api/SamProgram.cpp b/...src/utils/BamTools/src/api/SamProgram.cpp → ...src/utils/BamTools/src/api/SamProgram.cpp
diff --git a/...s/src/utils/BamTools/src/api/SamProgram.h → ...s/src/utils/BamTools/src/api/SamProgram.h b/...s/src/utils/BamTools/src/api/SamProgram.h → ...s/src/utils/BamTools/src/api/SamProgram.h
diff --git a/...tils/BamTools/src/api/SamProgramChain.cpp → ...tils/BamTools/src/api/SamProgramChain.cpp b/...tils/BamTools/src/api/SamProgramChain.cpp → ...tils/BamTools/src/api/SamProgramChain.cpp
diff --git a/.../utils/BamTools/src/api/SamProgramChain.h → .../utils/BamTools/src/api/SamProgramChain.h b/.../utils/BamTools/src/api/SamProgramChain.h → .../utils/BamTools/src/api/SamProgramChain.h
diff --git a/...c/utils/BamTools/src/api/SamReadGroup.cpp → ...c/utils/BamTools/src/api/SamReadGroup.cpp b/...c/utils/BamTools/src/api/SamReadGroup.cpp → ...c/utils/BamTools/src/api/SamReadGroup.cpp
diff --git a/...src/utils/BamTools/src/api/SamReadGroup.h → ...src/utils/BamTools/src/api/SamReadGroup.h b/...src/utils/BamTools/src/api/SamReadGroup.h → ...src/utils/BamTools/src/api/SamReadGroup.h
diff --git a/...mTools/src/api/SamReadGroupDictionary.cpp → ...mTools/src/api/SamReadGroupDictionary.cpp b/...mTools/src/api/SamReadGroupDictionary.cpp → ...mTools/src/api/SamReadGroupDictionary.cpp
diff --git a/...BamTools/src/api/SamReadGroupDictionary.h → ...BamTools/src/api/SamReadGroupDictionary.h b/...BamTools/src/api/SamReadGroupDictionary.h → ...BamTools/src/api/SamReadGroupDictionary.h
diff --git a/...rc/utils/BamTools/src/api/SamSequence.cpp → ...rc/utils/BamTools/src/api/SamSequence.cpp b/...rc/utils/BamTools/src/api/SamSequence.cpp → ...rc/utils/BamTools/src/api/SamSequence.cpp
diff --git a/.../src/utils/BamTools/src/api/SamSequence.h → .../src/utils/BamTools/src/api/SamSequence.h b/.../src/utils/BamTools/src/api/SamSequence.h → .../src/utils/BamTools/src/api/SamSequence.h
diff --git a/...amTools/src/api/SamSequenceDictionary.cpp → ...amTools/src/api/SamSequenceDictionary.cpp b/...amTools/src/api/SamSequenceDictionary.cpp → ...amTools/src/api/SamSequenceDictionary.cpp
diff --git a/.../BamTools/src/api/SamSequenceDictionary.h → .../BamTools/src/api/SamSequenceDictionary.h b/.../BamTools/src/api/SamSequenceDictionary.h → .../BamTools/src/api/SamSequenceDictionary.h
diff --git a/.../utils/BamTools/src/api/algorithms/Sort.h → .../utils/BamTools/src/api/algorithms/Sort.h b/.../utils/BamTools/src/api/algorithms/Sort.h → .../utils/BamTools/src/api/algorithms/Sort.h
diff --git a/...s/src/utils/BamTools/src/api/api_global.h → ...s/src/utils/BamTools/src/api/api_global.h b/...s/src/utils/BamTools/src/api/api_global.h → ...s/src/utils/BamTools/src/api/api_global.h
diff --git a/...ools/src/api/internal/bam/BamHeader_p.cpp → ...ools/src/api/internal/bam/BamHeader_p.cpp b/...ools/src/api/internal/bam/BamHeader_p.cpp → ...ools/src/api/internal/bam/BamHeader_p.cpp
diff --git a/...mTools/src/api/internal/bam/BamHeader_p.h → ...mTools/src/api/internal/bam/BamHeader_p.h b/...mTools/src/api/internal/bam/BamHeader_p.h → ...mTools/src/api/internal/bam/BamHeader_p.h
diff --git a/...s/src/api/internal/bam/BamMultiMerger_p.h → ...s/src/api/internal/bam/BamMultiMerger_p.h b/...s/src/api/internal/bam/BamMultiMerger_p.h → ...s/src/api/internal/bam/BamMultiMerger_p.h
diff --git a/...src/api/internal/bam/BamMultiReader_p.cpp → ...src/api/internal/bam/BamMultiReader_p.cpp b/...src/api/internal/bam/BamMultiReader_p.cpp → ...src/api/internal/bam/BamMultiReader_p.cpp
diff --git a/...s/src/api/internal/bam/BamMultiReader_p.h → ...s/src/api/internal/bam/BamMultiReader_p.h b/...s/src/api/internal/bam/BamMultiReader_p.h → ...s/src/api/internal/bam/BamMultiReader_p.h
diff --git a/...ernal/bam/BamRandomAccessController_p.cpp → ...ernal/bam/BamRandomAccessController_p.cpp b/...ernal/bam/BamRandomAccessController_p.cpp → ...ernal/bam/BamRandomAccessController_p.cpp
diff --git a/...nternal/bam/BamRandomAccessController_p.h → ...nternal/bam/BamRandomAccessController_p.h b/...nternal/bam/BamRandomAccessController_p.h → ...nternal/bam/BamRandomAccessController_p.h
diff --git a/...ools/src/api/internal/bam/BamReader_p.cpp → ...ools/src/api/internal/bam/BamReader_p.cpp b/...ools/src/api/internal/bam/BamReader_p.cpp → ...ools/src/api/internal/bam/BamReader_p.cpp
diff --git a/...mTools/src/api/internal/bam/BamReader_p.h → ...mTools/src/api/internal/bam/BamReader_p.h b/...mTools/src/api/internal/bam/BamReader_p.h → ...mTools/src/api/internal/bam/BamReader_p.h
diff --git a/...ools/src/api/internal/bam/BamWriter_p.cpp → ...ools/src/api/internal/bam/BamWriter_p.cpp b/...ools/src/api/internal/bam/BamWriter_p.cpp → ...ools/src/api/internal/bam/BamWriter_p.cpp
diff --git a/...mTools/src/api/internal/bam/BamWriter_p.h → ...mTools/src/api/internal/bam/BamWriter_p.h b/...mTools/src/api/internal/bam/BamWriter_p.h → ...mTools/src/api/internal/bam/BamWriter_p.h
diff --git a/.../api/internal/index/BamIndexFactory_p.cpp → .../api/internal/index/BamIndexFactory_p.cpp b/.../api/internal/index/BamIndexFactory_p.cpp → .../api/internal/index/BamIndexFactory_p.cpp
diff --git a/...rc/api/internal/index/BamIndexFactory_p.h → ...rc/api/internal/index/BamIndexFactory_p.h b/...rc/api/internal/index/BamIndexFactory_p.h → ...rc/api/internal/index/BamIndexFactory_p.h
diff --git a/...api/internal/index/BamStandardIndex_p.cpp → ...api/internal/index/BamStandardIndex_p.cpp b/...api/internal/index/BamStandardIndex_p.cpp → ...api/internal/index/BamStandardIndex_p.cpp
diff --git a/...c/api/internal/index/BamStandardIndex_p.h → ...c/api/internal/index/BamStandardIndex_p.h b/...c/api/internal/index/BamStandardIndex_p.h → ...c/api/internal/index/BamStandardIndex_p.h
diff --git a/...rc/api/internal/index/BamToolsIndex_p.cpp → ...rc/api/internal/index/BamToolsIndex_p.cpp b/...rc/api/internal/index/BamToolsIndex_p.cpp → ...rc/api/internal/index/BamToolsIndex_p.cpp
diff --git a/.../src/api/internal/index/BamToolsIndex_p.h → .../src/api/internal/index/BamToolsIndex_p.h b/.../src/api/internal/index/BamToolsIndex_p.h → .../src/api/internal/index/BamToolsIndex_p.h
diff --git a/...rc/api/internal/io/BamDeviceFactory_p.cpp → ...rc/api/internal/io/BamDeviceFactory_p.cpp b/...rc/api/internal/io/BamDeviceFactory_p.cpp → ...rc/api/internal/io/BamDeviceFactory_p.cpp
diff --git a/.../src/api/internal/io/BamDeviceFactory_p.h → .../src/api/internal/io/BamDeviceFactory_p.h b/.../src/api/internal/io/BamDeviceFactory_p.h → .../src/api/internal/io/BamDeviceFactory_p.h
diff --git a/...amTools/src/api/internal/io/BamFile_p.cpp → ...amTools/src/api/internal/io/BamFile_p.cpp b/...amTools/src/api/internal/io/BamFile_p.cpp → ...amTools/src/api/internal/io/BamFile_p.cpp
diff --git a/.../BamTools/src/api/internal/io/BamFile_p.h → .../BamTools/src/api/internal/io/BamFile_p.h b/.../BamTools/src/api/internal/io/BamFile_p.h → .../BamTools/src/api/internal/io/BamFile_p.h
diff --git a/...BamTools/src/api/internal/io/BamFtp_p.cpp → ...BamTools/src/api/internal/io/BamFtp_p.cpp b/...BamTools/src/api/internal/io/BamFtp_p.cpp → ...BamTools/src/api/internal/io/BamFtp_p.cpp
diff --git a/...s/BamTools/src/api/internal/io/BamFtp_p.h → ...s/BamTools/src/api/internal/io/BamFtp_p.h b/...s/BamTools/src/api/internal/io/BamFtp_p.h → ...s/BamTools/src/api/internal/io/BamFtp_p.h
diff --git a/...amTools/src/api/internal/io/BamHttp_p.cpp → ...amTools/src/api/internal/io/BamHttp_p.cpp b/...amTools/src/api/internal/io/BamHttp_p.cpp → ...amTools/src/api/internal/io/BamHttp_p.cpp
diff --git a/.../BamTools/src/api/internal/io/BamHttp_p.h → .../BamTools/src/api/internal/io/BamHttp_p.h b/.../BamTools/src/api/internal/io/BamHttp_p.h → .../BamTools/src/api/internal/io/BamHttp_p.h
diff --git a/...amTools/src/api/internal/io/BamPipe_p.cpp → ...amTools/src/api/internal/io/BamPipe_p.cpp b/...amTools/src/api/internal/io/BamPipe_p.cpp → ...amTools/src/api/internal/io/BamPipe_p.cpp
diff --git a/.../BamTools/src/api/internal/io/BamPipe_p.h → .../BamTools/src/api/internal/io/BamPipe_p.h b/.../BamTools/src/api/internal/io/BamPipe_p.h → .../BamTools/src/api/internal/io/BamPipe_p.h
diff --git a/...ools/src/api/internal/io/BgzfStream_p.cpp → ...ools/src/api/internal/io/BgzfStream_p.cpp b/...ools/src/api/internal/io/BgzfStream_p.cpp → ...ools/src/api/internal/io/BgzfStream_p.cpp
diff --git a/...mTools/src/api/internal/io/BgzfStream_p.h → ...mTools/src/api/internal/io/BgzfStream_p.h b/...mTools/src/api/internal/io/BgzfStream_p.h → ...mTools/src/api/internal/io/BgzfStream_p.h
diff --git a/...Tools/src/api/internal/io/ByteArray_p.cpp → ...Tools/src/api/internal/io/ByteArray_p.cpp b/...Tools/src/api/internal/io/ByteArray_p.cpp → ...Tools/src/api/internal/io/ByteArray_p.cpp
diff --git a/...amTools/src/api/internal/io/ByteArray_p.h → ...amTools/src/api/internal/io/ByteArray_p.h b/...amTools/src/api/internal/io/ByteArray_p.h → ...amTools/src/api/internal/io/ByteArray_p.h
diff --git a/...ols/src/api/internal/io/HostAddress_p.cpp → ...ols/src/api/internal/io/HostAddress_p.cpp b/...ols/src/api/internal/io/HostAddress_p.cpp → ...ols/src/api/internal/io/HostAddress_p.cpp
diff --git a/...Tools/src/api/internal/io/HostAddress_p.h → ...Tools/src/api/internal/io/HostAddress_p.h b/...Tools/src/api/internal/io/HostAddress_p.h → ...Tools/src/api/internal/io/HostAddress_p.h
diff --git a/...mTools/src/api/internal/io/HostInfo_p.cpp → ...mTools/src/api/internal/io/HostInfo_p.cpp b/...mTools/src/api/internal/io/HostInfo_p.cpp → ...mTools/src/api/internal/io/HostInfo_p.cpp
diff --git a/...BamTools/src/api/internal/io/HostInfo_p.h → ...BamTools/src/api/internal/io/HostInfo_p.h b/...BamTools/src/api/internal/io/HostInfo_p.h → ...BamTools/src/api/internal/io/HostInfo_p.h
diff --git a/...ools/src/api/internal/io/HttpHeader_p.cpp → ...ools/src/api/internal/io/HttpHeader_p.cpp b/...ools/src/api/internal/io/HttpHeader_p.cpp → ...ools/src/api/internal/io/HttpHeader_p.cpp
diff --git a/...mTools/src/api/internal/io/HttpHeader_p.h → ...mTools/src/api/internal/io/HttpHeader_p.h b/...mTools/src/api/internal/io/HttpHeader_p.h → ...mTools/src/api/internal/io/HttpHeader_p.h
diff --git a/.../src/api/internal/io/ILocalIODevice_p.cpp → .../src/api/internal/io/ILocalIODevice_p.cpp b/.../src/api/internal/io/ILocalIODevice_p.cpp → .../src/api/internal/io/ILocalIODevice_p.cpp
diff --git a/...ls/src/api/internal/io/ILocalIODevice_p.h → ...ls/src/api/internal/io/ILocalIODevice_p.h b/...ls/src/api/internal/io/ILocalIODevice_p.h → ...ls/src/api/internal/io/ILocalIODevice_p.h
diff --git a/.../BamTools/src/api/internal/io/NetUnix_p.h → .../BamTools/src/api/internal/io/NetUnix_p.h b/.../BamTools/src/api/internal/io/NetUnix_p.h → .../BamTools/src/api/internal/io/NetUnix_p.h
diff --git a/...s/BamTools/src/api/internal/io/NetWin_p.h → ...s/BamTools/src/api/internal/io/NetWin_p.h b/...s/BamTools/src/api/internal/io/NetWin_p.h → ...s/BamTools/src/api/internal/io/NetWin_p.h
diff --git a/...s/src/api/internal/io/RollingBuffer_p.cpp → ...s/src/api/internal/io/RollingBuffer_p.cpp b/...s/src/api/internal/io/RollingBuffer_p.cpp → ...s/src/api/internal/io/RollingBuffer_p.cpp
diff --git a/...ols/src/api/internal/io/RollingBuffer_p.h → ...ols/src/api/internal/io/RollingBuffer_p.h b/...ols/src/api/internal/io/RollingBuffer_p.h → ...ols/src/api/internal/io/RollingBuffer_p.h
diff --git a/...src/api/internal/io/TcpSocketEngine_p.cpp → ...src/api/internal/io/TcpSocketEngine_p.cpp b/...src/api/internal/io/TcpSocketEngine_p.cpp → ...src/api/internal/io/TcpSocketEngine_p.cpp
diff --git a/...s/src/api/internal/io/TcpSocketEngine_p.h → ...s/src/api/internal/io/TcpSocketEngine_p.h b/...s/src/api/internal/io/TcpSocketEngine_p.h → ...s/src/api/internal/io/TcpSocketEngine_p.h
diff --git a/...pi/internal/io/TcpSocketEngine_unix_p.cpp → ...pi/internal/io/TcpSocketEngine_unix_p.cpp b/...pi/internal/io/TcpSocketEngine_unix_p.cpp → ...pi/internal/io/TcpSocketEngine_unix_p.cpp
diff --git a/...api/internal/io/TcpSocketEngine_win_p.cpp → ...api/internal/io/TcpSocketEngine_win_p.cpp b/...api/internal/io/TcpSocketEngine_win_p.cpp → ...api/internal/io/TcpSocketEngine_win_p.cpp
diff --git a/...Tools/src/api/internal/io/TcpSocket_p.cpp → ...Tools/src/api/internal/io/TcpSocket_p.cpp b/...Tools/src/api/internal/io/TcpSocket_p.cpp → ...Tools/src/api/internal/io/TcpSocket_p.cpp
diff --git a/...amTools/src/api/internal/io/TcpSocket_p.h → ...amTools/src/api/internal/io/TcpSocket_p.h b/...amTools/src/api/internal/io/TcpSocket_p.h → ...amTools/src/api/internal/io/TcpSocket_p.h
diff --git a/...rc/api/internal/sam/SamFormatParser_p.cpp → ...rc/api/internal/sam/SamFormatParser_p.cpp b/...rc/api/internal/sam/SamFormatParser_p.cpp → ...rc/api/internal/sam/SamFormatParser_p.cpp
diff --git a/.../src/api/internal/sam/SamFormatParser_p.h → .../src/api/internal/sam/SamFormatParser_p.h b/.../src/api/internal/sam/SamFormatParser_p.h → .../src/api/internal/sam/SamFormatParser_p.h
diff --git a/...c/api/internal/sam/SamFormatPrinter_p.cpp → ...c/api/internal/sam/SamFormatPrinter_p.cpp b/...c/api/internal/sam/SamFormatPrinter_p.cpp → ...c/api/internal/sam/SamFormatPrinter_p.cpp
diff --git a/...src/api/internal/sam/SamFormatPrinter_p.h → ...src/api/internal/sam/SamFormatPrinter_p.h b/...src/api/internal/sam/SamFormatPrinter_p.h → ...src/api/internal/sam/SamFormatPrinter_p.h
diff --git a/...api/internal/sam/SamHeaderValidator_p.cpp → ...api/internal/sam/SamHeaderValidator_p.cpp b/...api/internal/sam/SamHeaderValidator_p.cpp → ...api/internal/sam/SamHeaderValidator_p.cpp
diff --git a/...c/api/internal/sam/SamHeaderValidator_p.h → ...c/api/internal/sam/SamHeaderValidator_p.h b/...c/api/internal/sam/SamHeaderValidator_p.h → ...c/api/internal/sam/SamHeaderValidator_p.h
diff --git a/...src/api/internal/sam/SamHeaderVersion_p.h → ...src/api/internal/sam/SamHeaderVersion_p.h b/...src/api/internal/sam/SamHeaderVersion_p.h → ...src/api/internal/sam/SamHeaderVersion_p.h
diff --git a/...src/api/internal/utils/BamException_p.cpp → ...src/api/internal/utils/BamException_p.cpp b/...src/api/internal/utils/BamException_p.cpp → ...src/api/internal/utils/BamException_p.cpp
diff --git a/...s/src/api/internal/utils/BamException_p.h → ...s/src/api/internal/utils/BamException_p.h b/...s/src/api/internal/utils/BamException_p.h → ...s/src/api/internal/utils/BamException_p.h
diff --git a/...ils/BamTools/src/shared/bamtools_global.h → ...ils/BamTools/src/shared/bamtools_global.h b/...ils/BamTools/src/shared/bamtools_global.h → ...ils/BamTools/src/shared/bamtools_global.h
diff --git a/...ils/BlockedIntervals/BlockedIntervals.cpp → ...ils/BlockedIntervals/BlockedIntervals.cpp b/...ils/BlockedIntervals/BlockedIntervals.cpp → ...ils/BlockedIntervals/BlockedIntervals.cpp
diff --git a/...utils/BlockedIntervals/BlockedIntervals.h → ...utils/BlockedIntervals/BlockedIntervals.h b/...utils/BlockedIntervals/BlockedIntervals.h → ...utils/BlockedIntervals/BlockedIntervals.h
diff --git a/...tools/src/utils/BlockedIntervals/Makefile → ...tools/src/utils/BlockedIntervals/Makefile b/...tools/src/utils/BlockedIntervals/Makefile → ...tools/src/utils/BlockedIntervals/Makefile
diff --git a/...ackage/bedtools/src/utils/Fasta/Fasta.cpp → ...ackage/bedtools/src/utils/Fasta/Fasta.cpp b/...ackage/bedtools/src/utils/Fasta/Fasta.cpp → ...ackage/bedtools/src/utils/Fasta/Fasta.cpp
diff --git a/...fpackage/bedtools/src/utils/Fasta/Fasta.h → ...fpackage/bedtools/src/utils/Fasta/Fasta.h b/...fpackage/bedtools/src/utils/Fasta/Fasta.h → ...fpackage/bedtools/src/utils/Fasta/Fasta.h
diff --git a/...dtools/src/utils/Fasta/LargeFileSupport.h → ...dtools/src/utils/Fasta/LargeFileSupport.h b/...dtools/src/utils/Fasta/LargeFileSupport.h → ...dtools/src/utils/Fasta/LargeFileSupport.h
diff --git a/...package/bedtools/src/utils/Fasta/Makefile → ...package/bedtools/src/utils/Fasta/Makefile b/...package/bedtools/src/utils/Fasta/Makefile → ...package/bedtools/src/utils/Fasta/Makefile
diff --git a/...ackage/bedtools/src/utils/Fasta/split.cpp → ...ackage/bedtools/src/utils/Fasta/split.cpp b/...ackage/bedtools/src/utils/Fasta/split.cpp → ...ackage/bedtools/src/utils/Fasta/split.cpp
diff --git a/...fpackage/bedtools/src/utils/Fasta/split.h → ...fpackage/bedtools/src/utils/Fasta/split.h b/...fpackage/bedtools/src/utils/Fasta/split.h → ...fpackage/bedtools/src/utils/Fasta/split.h
diff --git a/...fpackage/bedtools/src/utils/Point/Point.h → ...fpackage/bedtools/src/utils/Point/Point.h b/...fpackage/bedtools/src/utils/Point/Point.h → ...fpackage/bedtools/src/utils/Point/Point.h
diff --git a/...age/bedtools/src/utils/VectorOps/Makefile → ...age/bedtools/src/utils/VectorOps/Makefile b/...age/bedtools/src/utils/VectorOps/Makefile → ...age/bedtools/src/utils/VectorOps/Makefile
diff --git a/...edtools/src/utils/VectorOps/VectorOps.cpp → ...edtools/src/utils/VectorOps/VectorOps.cpp b/...edtools/src/utils/VectorOps/VectorOps.cpp → ...edtools/src/utils/VectorOps/VectorOps.cpp
diff --git a/.../bedtools/src/utils/VectorOps/VectorOps.h → .../bedtools/src/utils/VectorOps/VectorOps.h b/.../bedtools/src/utils/VectorOps/VectorOps.h → .../bedtools/src/utils/VectorOps/VectorOps.h
diff --git a/...ckage/bedtools/src/utils/bedFile/Makefile → ...ckage/bedtools/src/utils/bedFile/Makefile b/...ckage/bedtools/src/utils/bedFile/Makefile → ...ckage/bedtools/src/utils/bedFile/Makefile
diff --git a/...ge/bedtools/src/utils/bedFile/bedFile.cpp → ...ge/bedtools/src/utils/bedFile/bedFile.cpp b/...ge/bedtools/src/utils/bedFile/bedFile.cpp → ...ge/bedtools/src/utils/bedFile/bedFile.cpp
diff --git a/...kage/bedtools/src/utils/bedFile/bedFile.h → ...kage/bedtools/src/utils/bedFile/bedFile.h b/...kage/bedtools/src/utils/bedFile/bedFile.h → ...kage/bedtools/src/utils/bedFile/bedFile.h
diff --git a/...age/bedtools/src/utils/bedFilePE/Makefile → ...age/bedtools/src/utils/bedFilePE/Makefile b/...age/bedtools/src/utils/bedFilePE/Makefile → ...age/bedtools/src/utils/bedFilePE/Makefile
diff --git a/...edtools/src/utils/bedFilePE/bedFilePE.cpp → ...edtools/src/utils/bedFilePE/bedFilePE.cpp b/...edtools/src/utils/bedFilePE/bedFilePE.cpp → ...edtools/src/utils/bedFilePE/bedFilePE.cpp
diff --git a/.../bedtools/src/utils/bedFilePE/bedFilePE.h → .../bedtools/src/utils/bedFilePE/bedFilePE.h b/.../bedtools/src/utils/bedFilePE/bedFilePE.h → .../bedtools/src/utils/bedFilePE/bedFilePE.h
diff --git a/.../bedtools/src/utils/bedGraphFile/Makefile → .../bedtools/src/utils/bedGraphFile/Makefile b/.../bedtools/src/utils/bedGraphFile/Makefile → .../bedtools/src/utils/bedGraphFile/Makefile
diff --git a/...s/src/utils/bedGraphFile/bedGraphFile.cpp → ...s/src/utils/bedGraphFile/bedGraphFile.cpp b/...s/src/utils/bedGraphFile/bedGraphFile.cpp → ...s/src/utils/bedGraphFile/bedGraphFile.cpp
diff --git a/...ols/src/utils/bedGraphFile/bedGraphFile.h → ...ols/src/utils/bedGraphFile/bedGraphFile.h b/...ols/src/utils/bedGraphFile/bedGraphFile.h → ...ols/src/utils/bedGraphFile/bedGraphFile.h
diff --git a/...ge/bedtools/src/utils/chromsweep/Makefile → ...ge/bedtools/src/utils/chromsweep/Makefile b/...ge/bedtools/src/utils/chromsweep/Makefile → ...ge/bedtools/src/utils/chromsweep/Makefile
diff --git a/...tools/src/utils/chromsweep/chromsweep.cpp → ...tools/src/utils/chromsweep/chromsweep.cpp b/...tools/src/utils/chromsweep/chromsweep.cpp → ...tools/src/utils/chromsweep/chromsweep.cpp
diff --git a/...edtools/src/utils/chromsweep/chromsweep.h → ...edtools/src/utils/chromsweep/chromsweep.h b/...edtools/src/utils/chromsweep/chromsweep.h → ...edtools/src/utils/chromsweep/chromsweep.h
diff --git a/...kage/bedtools/src/utils/fileType/Makefile → ...kage/bedtools/src/utils/fileType/Makefile b/...kage/bedtools/src/utils/fileType/Makefile → ...kage/bedtools/src/utils/fileType/Makefile
diff --git a/.../bedtools/src/utils/fileType/fileType.cpp → .../bedtools/src/utils/fileType/fileType.cpp b/.../bedtools/src/utils/fileType/fileType.cpp → .../bedtools/src/utils/fileType/fileType.cpp
diff --git a/...ge/bedtools/src/utils/fileType/fileType.h → ...ge/bedtools/src/utils/fileType/fileType.h b/...ge/bedtools/src/utils/fileType/fileType.h → ...ge/bedtools/src/utils/fileType/fileType.h
diff --git a/...ge/bedtools/src/utils/genomeFile/Makefile → ...ge/bedtools/src/utils/genomeFile/Makefile b/...ge/bedtools/src/utils/genomeFile/Makefile → ...ge/bedtools/src/utils/genomeFile/Makefile
diff --git a/...tools/src/utils/genomeFile/genomeFile.cpp → ...tools/src/utils/genomeFile/genomeFile.cpp b/...tools/src/utils/genomeFile/genomeFile.cpp → ...tools/src/utils/genomeFile/genomeFile.cpp
diff --git a/...edtools/src/utils/genomeFile/genomeFile.h → ...edtools/src/utils/genomeFile/genomeFile.h b/...edtools/src/utils/genomeFile/genomeFile.h → ...edtools/src/utils/genomeFile/genomeFile.h
diff --git a/...e/bedtools/src/utils/gzstream/COPYING.LIB → ...e/bedtools/src/utils/gzstream/COPYING.LIB b/...e/bedtools/src/utils/gzstream/COPYING.LIB → ...e/bedtools/src/utils/gzstream/COPYING.LIB
diff --git a/...kage/bedtools/src/utils/gzstream/Makefile → ...kage/bedtools/src/utils/gzstream/Makefile b/...kage/bedtools/src/utils/gzstream/Makefile → ...kage/bedtools/src/utils/gzstream/Makefile
diff --git a/...ackage/bedtools/src/utils/gzstream/README → ...ackage/bedtools/src/utils/gzstream/README b/...ackage/bedtools/src/utils/gzstream/README → ...ackage/bedtools/src/utils/gzstream/README
diff --git a/...ge/bedtools/src/utils/gzstream/gzstream.C → ...ge/bedtools/src/utils/gzstream/gzstream.C b/...ge/bedtools/src/utils/gzstream/gzstream.C → ...ge/bedtools/src/utils/gzstream/gzstream.C
diff --git a/...ge/bedtools/src/utils/gzstream/gzstream.h → ...ge/bedtools/src/utils/gzstream/gzstream.h b/...ge/bedtools/src/utils/gzstream/gzstream.h → ...ge/bedtools/src/utils/gzstream/gzstream.h
diff --git a/...ckage/bedtools/src/utils/gzstream/version → ...ckage/bedtools/src/utils/gzstream/version b/...ckage/bedtools/src/utils/gzstream/version → ...ckage/bedtools/src/utils/gzstream/version
diff --git a/...ils/lineFileUtilities/lineFileUtilities.h → ...ils/lineFileUtilities/lineFileUtilities.h b/...ils/lineFileUtilities/lineFileUtilities.h → ...ils/lineFileUtilities/lineFileUtilities.h