ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/.svn/entries

@@ -0,0 +1,708 @@
+10
+
+dir
+620
+https://vcftools.svn.sourceforge.net/svnroot/vcftools/cpp
+https://vcftools.svn.sourceforge.net/svnroot/vcftools
+
+
+
+2011-10-06T16:08:21.100852Z
+620
+auton1
+has-props
+
+
+
+
+
+
+
+
+
+
+
+
+
+9c269a97-bb8f-4c93-a6da-4cfa3dbe9892
+
+vcf_entry.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+f7e46d823e2cca2529f4f8c8c4f80f8d
+2011-09-26T12:02:03.058786Z
+611
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+13625
+
+dgeev.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+3f4996d60e13ccf83c343bbc5f99e3b0
+2011-04-20T10:09:42.135482Z
+508
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1531
+
+vcftools.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+0ea4222aa49912197a1b8fbc9f52a2bf
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+6210
+
+output_log.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+8253fa31256e0e59576188a9da2926ae
+2011-03-01T14:07:05.370573Z
+457
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1359
+
+parameters.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+135150c42eea520d673b11b17a396f3e
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+29887
+
+vcf_entry.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+1addfcca0261e8e0a771a73bb2f1a78f
+2011-06-28T09:59:57.531572Z
+546
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+6449
+
+vcf_file_index.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+4d450a60fbecdd01bc13b6686f63325c
+2011-08-10T09:19:53.172450Z
+584
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+3911
+
+vcftools.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+689f9e65ae7110e788d9deda1f4c4427
+2010-07-07T10:23:40.308843Z
+259
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+377
+
+vcf_file_filters.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+3300c99ca519abe8b458cd43ef5ca3a7
+2011-10-06T10:47:56.980107Z
+619
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+31536
+
+vcf_file_diff.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+2c0896a1aefac4465a90b59c82c28794
+2011-07-05T11:03:00.864035Z
+555
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+42519
+
+output_log.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+59192906773fe77e54dd3c17de1b68c7
+2011-03-01T14:07:05.370573Z
+457
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+674
+
+vcf_entry_setters.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+0f68e5aced750dd40cfc98baca8588a4
+2011-09-26T12:53:10.672873Z
+612
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+11365
+
+parameters.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+f2aae9a0aa0862c9e8c521d7b39a55f1
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+3458
+
+vcf_file.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+c2bfa1d77f92b12d0471d987fac831b6
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+11914
+
+vcf_file.h
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+59ddccc77d49148ea589e483964dbe5f
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+8477
+
+vcf_file_format_convert.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+61b61e8b00c50eda66cb085b59e0419b
+2011-06-28T11:25:38.597217Z
+547
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+29277
+
+dgeev.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+7c3b2f52bc31774723925cf9cbcdcf30
+2011-04-20T10:09:42.135482Z
+508
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+2975
+
+vcf_entry_getters.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+f069a3751fffe4a37014b8fd857b3d3f
+2011-09-26T12:53:10.672873Z
+612
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+8428
+
+Makefile
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+68c294a8543cd7db1b078972bd393299
+2011-08-03T14:40:13.351151Z
+575
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+1009
+
+vcf_file_output.cpp
+file
+
+
+
+
+2011-10-07T08:38:39.000000Z
+f7d775af57ba303fa955cd4a72255fb3
+2011-10-06T16:08:21.100852Z
+620
+auton1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+80715
+

data/ext/vcftools/cpp/.svn/text-base/Makefile.svn-base

@@ -0,0 +1,46 @@
+# Make file for vcftools
+# Author: Adam Auton
+# ($Revision: 230 $)
+
+# Compiler
+CPP = g++
+# Output executable
+EXECUTABLE = vcftools
+# Flag used to turn on compilation of PCA routines
+ifndef VCFTOOLS_PCA
+	VCFTOOLS_PCA = 0
+endif
+# Compiler flags
+CPPFLAGS = -O2 -Wall -Wextra
+#CPPFLAGS = -g 
+# Included libraries (zlib)
+LIB = -lz 
+#LIB = -lz -I/opt/local/include/ -L/opt/local/lib/
+SOURCES = vcftools.cpp vcf_file.cpp vcf_entry.cpp \
+			vcf_entry_getters.cpp vcf_entry_setters.cpp \
+			vcf_file_filters.cpp vcf_file_output.cpp \
+			vcf_file_format_convert.cpp \
+			vcf_file_diff.cpp parameters.cpp \
+			vcf_file_index.cpp \
+			output_log.cpp
+
+ifeq ($(VCFTOOLS_PCA), 1)
+	# Define flag for PCA routine compilation
+	CPPFLAGS += -DVCFTOOLS_PCA
+	# Add LAPACK library
+	LIB += -llapack	
+	# Add PCA source code
+	SOURCES += dgeev.cpp
+endif
+
+all: vcftools
+
+vcftools: $(SOURCES)
+	$(CPP) $(CPPFLAGS) $(SOURCES) -o $@ $(LIB)
+ifdef BINDIR
+	cp $(CURDIR)/$@ $(BINDIR)/$@
+endif
+
+clean:
+	@rm -f vcftools
+	@rm -f $(BINDIR)/vcftools