From e7aeb5bd7a4d3b05f7e052defd021843e9b4b8c0 Mon Sep 17 00:00:00 2001
From: "Aflitos, Saulo Alves" <sauloalves.aflitos@wur.nl>
Date: Mon, 1 Jun 2015 17:59:23 +0200
Subject: [PATCH] converter for multicolumn vcf
---
vcfmerger/.gitignore | 1 +
vcfmerger/{aux => }/Consolas.ttf | Bin
vcfmerger/{aux => }/FastTreeMP | Bin
vcfmerger/aux/.gitignore | 1 -
vcfmerger/{aux => }/copy.sh | 0
vcfmerger/{aux => }/countUnique.sh | 0
vcfmerger/{aux => }/covmerger/README.md | 0
vcfmerger/{aux => }/covmerger/covMerger | Bin
vcfmerger/{aux => }/covmerger/covMerger.cpp | 0
vcfmerger/{aux => }/covmerger/covMergerMake.sh | 0
vcfmerger/{aux => }/covmerger/filter.py | 0
vcfmerger/{aux => }/covmerger/gzstream.h | 0
vcfmerger/{aux => }/covmerger/gzstream/COPYING.LIB | 0
vcfmerger/{aux => }/covmerger/gzstream/Makefile | 0
vcfmerger/{aux => }/covmerger/gzstream/README | 0
vcfmerger/{aux => }/covmerger/gzstream/gzstream.C | 0
vcfmerger/{aux => }/covmerger/gzstream/gzstream.h | 0
vcfmerger/{aux => }/covmerger/gzstream/index.html | 0
.../{aux => }/covmerger/gzstream/libgzstream.a | Bin
vcfmerger/{aux => }/covmerger/gzstream/logo.gif | Bin
vcfmerger/{aux => }/covmerger/gzstream/test_gunzip | Bin
.../{aux => }/covmerger/gzstream/test_gunzip.C | 0
vcfmerger/{aux => }/covmerger/gzstream/test_gzip | Bin
vcfmerger/{aux => }/covmerger/gzstream/test_gzip.C | 0
vcfmerger/{aux => }/covmerger/gzstream/version | 0
vcfmerger/{aux => }/covmerger/range | Bin
vcfmerger/{aux => }/covmerger/range.cpp | 0
vcfmerger/{aux => }/covmerger/rangeMake.sh | 0
vcfmerger/{aux => }/covmerger/test_arcanum.lst | 0
.../covmerger/test_arcanum.lst.filtered.cov | 0
.../covmerger/test_arcanum.lst.filtered.gff3 | 0
vcfmerger/{aux => }/dbprinter.py | 0
vcfmerger/{aux => }/fasta_spacer.py | 0
vcfmerger/{aux => }/filterpos.sh | 0
vcfmerger/{aux => }/filterposall.sh | 0
vcfmerger/{aux => }/gen_makefile.py | 0
vcfmerger/{aux => }/gen_makefile.py.examples | 0
vcfmerger/{aux => }/makefile2dot.py | 0
vcfmerger/{aux => }/matrix_dists.py | 0
vcfmerger/{aux => }/mkrandomgenelist.sh | 0
vcfmerger/{aux => }/pngfolder_to_html.py | 0
vcfmerger/{aux => }/py-editdist-0.3/ChangeLog | 0
vcfmerger/{aux => }/py-editdist-0.3/LICENSE | 0
vcfmerger/{aux => }/py-editdist-0.3/MANIFEST | 0
vcfmerger/{aux => }/py-editdist-0.3/PKG-INFO | 0
vcfmerger/{aux => }/py-editdist-0.3/README | 0
vcfmerger/{aux => }/py-editdist-0.3/TODO | 0
vcfmerger/{aux => }/py-editdist-0.3/editdist.c | 0
.../{aux => }/py-editdist-0.3/py-editdist.spec | 0
vcfmerger/{aux => }/py-editdist-0.3/setup.py | 0
vcfmerger/{aux => }/py-editdist-0.3/test.py | 0
vcfmerger/{aux => }/tosql.sh | 0
52 files changed, 1 insertion(+), 1 deletion(-)
rename vcfmerger/{aux => }/Consolas.ttf (100%)
rename vcfmerger/{aux => }/FastTreeMP (100%)
delete mode 100644 vcfmerger/aux/.gitignore
rename vcfmerger/{aux => }/copy.sh (100%)
rename vcfmerger/{aux => }/countUnique.sh (100%)
rename vcfmerger/{aux => }/covmerger/README.md (100%)
rename vcfmerger/{aux => }/covmerger/covMerger (100%)
rename vcfmerger/{aux => }/covmerger/covMerger.cpp (100%)
rename vcfmerger/{aux => }/covmerger/covMergerMake.sh (100%)
rename vcfmerger/{aux => }/covmerger/filter.py (100%)
rename vcfmerger/{aux => }/covmerger/gzstream.h (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/COPYING.LIB (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/Makefile (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/README (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/gzstream.C (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/gzstream.h (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/index.html (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/libgzstream.a (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/logo.gif (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/test_gunzip (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/test_gunzip.C (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/test_gzip (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/test_gzip.C (100%)
rename vcfmerger/{aux => }/covmerger/gzstream/version (100%)
rename vcfmerger/{aux => }/covmerger/range (100%)
rename vcfmerger/{aux => }/covmerger/range.cpp (100%)
rename vcfmerger/{aux => }/covmerger/rangeMake.sh (100%)
rename vcfmerger/{aux => }/covmerger/test_arcanum.lst (100%)
rename vcfmerger/{aux => }/covmerger/test_arcanum.lst.filtered.cov (100%)
rename vcfmerger/{aux => }/covmerger/test_arcanum.lst.filtered.gff3 (100%)
rename vcfmerger/{aux => }/dbprinter.py (100%)
rename vcfmerger/{aux => }/fasta_spacer.py (100%)
rename vcfmerger/{aux => }/filterpos.sh (100%)
rename vcfmerger/{aux => }/filterposall.sh (100%)
rename vcfmerger/{aux => }/gen_makefile.py (100%)
rename vcfmerger/{aux => }/gen_makefile.py.examples (100%)
rename vcfmerger/{aux => }/makefile2dot.py (100%)
rename vcfmerger/{aux => }/matrix_dists.py (100%)
rename vcfmerger/{aux => }/mkrandomgenelist.sh (100%)
rename vcfmerger/{aux => }/pngfolder_to_html.py (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/ChangeLog (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/LICENSE (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/MANIFEST (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/PKG-INFO (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/README (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/TODO (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/editdist.c (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/py-editdist.spec (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/setup.py (100%)
rename vcfmerger/{aux => }/py-editdist-0.3/test.py (100%)
rename vcfmerger/{aux => }/tosql.sh (100%)
diff --git a/vcfmerger/.gitignore b/vcfmerger/.gitignore
index 99cea35..fb12b71 100644
--- a/vcfmerger/.gitignore
+++ b/vcfmerger/.gitignore
@@ -1,3 +1,4 @@
*.pickle.gz
*.svg
*.pyc
+pypy-2.3.1-linux64
diff --git a/vcfmerger/aux/Consolas.ttf b/vcfmerger/Consolas.ttf
similarity index 100%
rename from vcfmerger/aux/Consolas.ttf
rename to vcfmerger/Consolas.ttf
diff --git a/vcfmerger/aux/FastTreeMP b/vcfmerger/FastTreeMP
similarity index 100%
rename from vcfmerger/aux/FastTreeMP
rename to vcfmerger/FastTreeMP
diff --git a/vcfmerger/aux/.gitignore b/vcfmerger/aux/.gitignore
deleted file mode 100644
index 78a5930..0000000
--- a/vcfmerger/aux/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-pypy-2.3.1-linux64
diff --git a/vcfmerger/aux/copy.sh b/vcfmerger/copy.sh
similarity index 100%
rename from vcfmerger/aux/copy.sh
rename to vcfmerger/copy.sh
diff --git a/vcfmerger/aux/countUnique.sh b/vcfmerger/countUnique.sh
similarity index 100%
rename from vcfmerger/aux/countUnique.sh
rename to vcfmerger/countUnique.sh
diff --git a/vcfmerger/aux/covmerger/README.md b/vcfmerger/covmerger/README.md
similarity index 100%
rename from vcfmerger/aux/covmerger/README.md
rename to vcfmerger/covmerger/README.md
diff --git a/vcfmerger/aux/covmerger/covMerger b/vcfmerger/covmerger/covMerger
similarity index 100%
rename from vcfmerger/aux/covmerger/covMerger
rename to vcfmerger/covmerger/covMerger
diff --git a/vcfmerger/aux/covmerger/covMerger.cpp b/vcfmerger/covmerger/covMerger.cpp
similarity index 100%
rename from vcfmerger/aux/covmerger/covMerger.cpp
rename to vcfmerger/covmerger/covMerger.cpp
diff --git a/vcfmerger/aux/covmerger/covMergerMake.sh b/vcfmerger/covmerger/covMergerMake.sh
similarity index 100%
rename from vcfmerger/aux/covmerger/covMergerMake.sh
rename to vcfmerger/covmerger/covMergerMake.sh
diff --git a/vcfmerger/aux/covmerger/filter.py b/vcfmerger/covmerger/filter.py
similarity index 100%
rename from vcfmerger/aux/covmerger/filter.py
rename to vcfmerger/covmerger/filter.py
diff --git a/vcfmerger/aux/covmerger/gzstream.h b/vcfmerger/covmerger/gzstream.h
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream.h
rename to vcfmerger/covmerger/gzstream.h
diff --git a/vcfmerger/aux/covmerger/gzstream/COPYING.LIB b/vcfmerger/covmerger/gzstream/COPYING.LIB
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/COPYING.LIB
rename to vcfmerger/covmerger/gzstream/COPYING.LIB
diff --git a/vcfmerger/aux/covmerger/gzstream/Makefile b/vcfmerger/covmerger/gzstream/Makefile
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/Makefile
rename to vcfmerger/covmerger/gzstream/Makefile
diff --git a/vcfmerger/aux/covmerger/gzstream/README b/vcfmerger/covmerger/gzstream/README
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/README
rename to vcfmerger/covmerger/gzstream/README
diff --git a/vcfmerger/aux/covmerger/gzstream/gzstream.C b/vcfmerger/covmerger/gzstream/gzstream.C
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/gzstream.C
rename to vcfmerger/covmerger/gzstream/gzstream.C
diff --git a/vcfmerger/aux/covmerger/gzstream/gzstream.h b/vcfmerger/covmerger/gzstream/gzstream.h
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/gzstream.h
rename to vcfmerger/covmerger/gzstream/gzstream.h
diff --git a/vcfmerger/aux/covmerger/gzstream/index.html b/vcfmerger/covmerger/gzstream/index.html
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/index.html
rename to vcfmerger/covmerger/gzstream/index.html
diff --git a/vcfmerger/aux/covmerger/gzstream/libgzstream.a b/vcfmerger/covmerger/gzstream/libgzstream.a
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/libgzstream.a
rename to vcfmerger/covmerger/gzstream/libgzstream.a
diff --git a/vcfmerger/aux/covmerger/gzstream/logo.gif b/vcfmerger/covmerger/gzstream/logo.gif
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/logo.gif
rename to vcfmerger/covmerger/gzstream/logo.gif
diff --git a/vcfmerger/aux/covmerger/gzstream/test_gunzip b/vcfmerger/covmerger/gzstream/test_gunzip
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/test_gunzip
rename to vcfmerger/covmerger/gzstream/test_gunzip
diff --git a/vcfmerger/aux/covmerger/gzstream/test_gunzip.C b/vcfmerger/covmerger/gzstream/test_gunzip.C
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/test_gunzip.C
rename to vcfmerger/covmerger/gzstream/test_gunzip.C
diff --git a/vcfmerger/aux/covmerger/gzstream/test_gzip b/vcfmerger/covmerger/gzstream/test_gzip
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/test_gzip
rename to vcfmerger/covmerger/gzstream/test_gzip
diff --git a/vcfmerger/aux/covmerger/gzstream/test_gzip.C b/vcfmerger/covmerger/gzstream/test_gzip.C
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/test_gzip.C
rename to vcfmerger/covmerger/gzstream/test_gzip.C
diff --git a/vcfmerger/aux/covmerger/gzstream/version b/vcfmerger/covmerger/gzstream/version
similarity index 100%
rename from vcfmerger/aux/covmerger/gzstream/version
rename to vcfmerger/covmerger/gzstream/version
diff --git a/vcfmerger/aux/covmerger/range b/vcfmerger/covmerger/range
similarity index 100%
rename from vcfmerger/aux/covmerger/range
rename to vcfmerger/covmerger/range
diff --git a/vcfmerger/aux/covmerger/range.cpp b/vcfmerger/covmerger/range.cpp
similarity index 100%
rename from vcfmerger/aux/covmerger/range.cpp
rename to vcfmerger/covmerger/range.cpp
diff --git a/vcfmerger/aux/covmerger/rangeMake.sh b/vcfmerger/covmerger/rangeMake.sh
similarity index 100%
rename from vcfmerger/aux/covmerger/rangeMake.sh
rename to vcfmerger/covmerger/rangeMake.sh
diff --git a/vcfmerger/aux/covmerger/test_arcanum.lst b/vcfmerger/covmerger/test_arcanum.lst
similarity index 100%
rename from vcfmerger/aux/covmerger/test_arcanum.lst
rename to vcfmerger/covmerger/test_arcanum.lst
diff --git a/vcfmerger/aux/covmerger/test_arcanum.lst.filtered.cov b/vcfmerger/covmerger/test_arcanum.lst.filtered.cov
similarity index 100%
rename from vcfmerger/aux/covmerger/test_arcanum.lst.filtered.cov
rename to vcfmerger/covmerger/test_arcanum.lst.filtered.cov
diff --git a/vcfmerger/aux/covmerger/test_arcanum.lst.filtered.gff3 b/vcfmerger/covmerger/test_arcanum.lst.filtered.gff3
similarity index 100%
rename from vcfmerger/aux/covmerger/test_arcanum.lst.filtered.gff3
rename to vcfmerger/covmerger/test_arcanum.lst.filtered.gff3
diff --git a/vcfmerger/aux/dbprinter.py b/vcfmerger/dbprinter.py
similarity index 100%
rename from vcfmerger/aux/dbprinter.py
rename to vcfmerger/dbprinter.py
diff --git a/vcfmerger/aux/fasta_spacer.py b/vcfmerger/fasta_spacer.py
similarity index 100%
rename from vcfmerger/aux/fasta_spacer.py
rename to vcfmerger/fasta_spacer.py
diff --git a/vcfmerger/aux/filterpos.sh b/vcfmerger/filterpos.sh
similarity index 100%
rename from vcfmerger/aux/filterpos.sh
rename to vcfmerger/filterpos.sh
diff --git a/vcfmerger/aux/filterposall.sh b/vcfmerger/filterposall.sh
similarity index 100%
rename from vcfmerger/aux/filterposall.sh
rename to vcfmerger/filterposall.sh
diff --git a/vcfmerger/aux/gen_makefile.py b/vcfmerger/gen_makefile.py
similarity index 100%
rename from vcfmerger/aux/gen_makefile.py
rename to vcfmerger/gen_makefile.py
diff --git a/vcfmerger/aux/gen_makefile.py.examples b/vcfmerger/gen_makefile.py.examples
similarity index 100%
rename from vcfmerger/aux/gen_makefile.py.examples
rename to vcfmerger/gen_makefile.py.examples
diff --git a/vcfmerger/aux/makefile2dot.py b/vcfmerger/makefile2dot.py
similarity index 100%
rename from vcfmerger/aux/makefile2dot.py
rename to vcfmerger/makefile2dot.py
diff --git a/vcfmerger/aux/matrix_dists.py b/vcfmerger/matrix_dists.py
similarity index 100%
rename from vcfmerger/aux/matrix_dists.py
rename to vcfmerger/matrix_dists.py
diff --git a/vcfmerger/aux/mkrandomgenelist.sh b/vcfmerger/mkrandomgenelist.sh
similarity index 100%
rename from vcfmerger/aux/mkrandomgenelist.sh
rename to vcfmerger/mkrandomgenelist.sh
diff --git a/vcfmerger/aux/pngfolder_to_html.py b/vcfmerger/pngfolder_to_html.py
similarity index 100%
rename from vcfmerger/aux/pngfolder_to_html.py
rename to vcfmerger/pngfolder_to_html.py
diff --git a/vcfmerger/aux/py-editdist-0.3/ChangeLog b/vcfmerger/py-editdist-0.3/ChangeLog
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/ChangeLog
rename to vcfmerger/py-editdist-0.3/ChangeLog
diff --git a/vcfmerger/aux/py-editdist-0.3/LICENSE b/vcfmerger/py-editdist-0.3/LICENSE
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/LICENSE
rename to vcfmerger/py-editdist-0.3/LICENSE
diff --git a/vcfmerger/aux/py-editdist-0.3/MANIFEST b/vcfmerger/py-editdist-0.3/MANIFEST
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/MANIFEST
rename to vcfmerger/py-editdist-0.3/MANIFEST
diff --git a/vcfmerger/aux/py-editdist-0.3/PKG-INFO b/vcfmerger/py-editdist-0.3/PKG-INFO
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/PKG-INFO
rename to vcfmerger/py-editdist-0.3/PKG-INFO
diff --git a/vcfmerger/aux/py-editdist-0.3/README b/vcfmerger/py-editdist-0.3/README
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/README
rename to vcfmerger/py-editdist-0.3/README
diff --git a/vcfmerger/aux/py-editdist-0.3/TODO b/vcfmerger/py-editdist-0.3/TODO
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/TODO
rename to vcfmerger/py-editdist-0.3/TODO
diff --git a/vcfmerger/aux/py-editdist-0.3/editdist.c b/vcfmerger/py-editdist-0.3/editdist.c
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/editdist.c
rename to vcfmerger/py-editdist-0.3/editdist.c
diff --git a/vcfmerger/aux/py-editdist-0.3/py-editdist.spec b/vcfmerger/py-editdist-0.3/py-editdist.spec
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/py-editdist.spec
rename to vcfmerger/py-editdist-0.3/py-editdist.spec
diff --git a/vcfmerger/aux/py-editdist-0.3/setup.py b/vcfmerger/py-editdist-0.3/setup.py
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/setup.py
rename to vcfmerger/py-editdist-0.3/setup.py
diff --git a/vcfmerger/aux/py-editdist-0.3/test.py b/vcfmerger/py-editdist-0.3/test.py
similarity index 100%
rename from vcfmerger/aux/py-editdist-0.3/test.py
rename to vcfmerger/py-editdist-0.3/test.py
diff --git a/vcfmerger/aux/tosql.sh b/vcfmerger/tosql.sh
similarity index 100%
rename from vcfmerger/aux/tosql.sh
rename to vcfmerger/tosql.sh
--
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