Merge pull request #5 from aylingm/master

Merged Martin's Final Pull Request
richardmleggett · Dec 13, 2017 · 346ce5f · 346ce5f
2 parents bf4c30a + 12b4831
commit 346ce5f
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Showing 173 changed files with 18,499 additions and 4,442 deletions.
diff --git a/.Rhistory b/.Rhistory
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,5 @@ obj
 bin
 src/cortex/metacortex_old.c
 src/cortex/metacortex_new.c
+.Rhistory
+.DS_Store
diff --git a/LICENSE b/LICENSE
diff --git a/Makefile b/Makefile
@@ -5,52 +5,47 @@ ifndef CC
 endif
 
 ifdef MAC
-    # Change the following to point to your GCC binary
-    CC=/usr/local/Cellar/gcc/4.9.2_1/bin/gcc-4.9
-    #MACFLAG = -fnested-functions
+    $(warning On MacOS, make sure you set CC to point to your GCC binary - LLVM won't compile MetaCortex)
+    $(warning     e.g. export CC=/usr/local/Cellar/gcc/7.1.0/bin/gcc-7)
 endif
 
 BIN = bin
 LIB = lib
 
-ifeq ($(MAXK),31)
-   BITFIELDS = 1
-endif
-
-ifeq ($(MAXK),63)
-   BITFIELDS = 2
-endif
-
-ifeq ($(MAXK),95)
-   BITFIELDS = 3
-endif
-
-ifeq ($(MAXK),127)
-   BITFIELDS = 4
-endif
-
-ifeq ($(MAXK),160)
-   BITFIELDS = 5
-endif
-
-ifeq ($(MAXK),192)
-   BITFIELDS = 6
-endif
-
-ifeq ($(MAXK),223)
-   BITFIELDS = 7
-endif
-
-ifeq ($(MAXK),255)
-   BITFIELDS = 8
-endif
-
-ifndef BITFIELDS
-   BITFIELDS = 1
-   MAXK = 31
-endif
-
-BIN_SUFFIX = $(MAXK)
+ifndef MAXK
+ MAXK = 31
+endif
+
+ifeq ($(shell expr $(MAXK) \< 32),1)
+BITFIELDS = 1
+BIN_SUFFIX=31
+else ifeq ($(shell expr $(MAXK) \< 64),1)
+BITFIELDS = 2
+BIN_SUFFIX=63
+else ifeq ($(shell expr $(MAXK) \< 96),1)
+BITFIELDS = 3
+BIN_SUFFIX=95
+else ifeq ($(shell expr $(MAXK) \< 128),1)
+BITFIELDS = 4
+BIN_SUFFIX=127
+else ifeq ($(shell expr $(MAXK) \< 161),1)
+BITFIELDS = 5
+BIN_SUFFIX=159
+else ifeq ($(shell expr $(MAXK) \< 193),1)
+BITFIELDS = 6
+BIN_SUFFIX=191
+else ifeq ($(shell expr $(MAXK) \< 224),1)
+BITFIELDS = 7
+BIN_SUFFIX=223
+else ifeq ($(shell expr $(MAXK) \< 256),1)
+BITFIELDS = 8
+BIN_SUFFIX=255
+else
+BITFIELDS = 1
+BIN_SUFFIX=31
+endif
+
+#BIN_SUFFIX = $(MAXK)
 
 # Main program includes
 IDIR_BASIC =include/basic
@@ -89,10 +84,11 @@ ifdef 32_BITS
 endif
 
 # Compiler options
-OPT		= $(ARCH) -Wall -O3 $(MACFLAG) -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -pthread -g
+OPT		= $(ARCH) -Wall -O3 -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -pthread -g
+#-Wno-duplicate-decl-specifier
 
 ifdef DEBUG
-OPT	= $(ARCH) -Wall -O0 $(MACFLAG) -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -g -pthread
+OPT	= $(ARCH) -Wall -O0 -DNUMBER_OF_BITFIELDS_IN_BINARY_KMER=$(BITFIELDS) -g -pthread
 endif
 
 ifdef DEBUG_PRINT_LABELS
@@ -114,7 +110,7 @@ CFLAGS_METACORTEX_TESTS	= -I$(IDIR_CUNIT) $(CFLAGS_CUNIT) -I$(IDIR_BASIC) -I$(ID
 CFLAGS_BASIC_TESTS = -I$(IDIR_CUNIT) $(CFLAGS_CUNIT) -I$(IDIR_BASIC) -I$(IDIR_BASIC_TESTS)
 
 # Program objects
-METACORTEX_OBJ = obj/cortex/file_format.o obj/cortex/flags.o obj/cortex/cleaning.o obj/cortex/path.o obj/cortex/perfect_path.o obj/cortex/branches.o obj/cortex/y_walk.o obj/cortex/cmd_line.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_value.o obj/cortex/hash_table.o obj/cortex/dB_graph.o obj/cortex/file_reader.o obj/cortex/metacortex.o obj/cortex/logger.o obj/cortex/metagraphs.o obj/cortex/coverage_walk.o obj/util/node_queue.o obj/cortex/graph_stats.o obj/cortex/bubble_find.o
+METACORTEX_OBJ = obj/cortex/file_format.o obj/cortex/flags.o obj/cortex/cleaning.o obj/cortex/path.o obj/cortex/perfect_path.o obj/cortex/branches.o obj/cortex/y_walk.o obj/cortex/cmd_line.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_value.o obj/cortex/hash_table.o obj/cortex/dB_graph.o obj/cortex/file_reader.o obj/cortex/metacortex.o obj/cortex/logger.o obj/cortex/metagraphs.o obj/cortex/coverage_walk.o obj/util/node_queue.o obj/cortex/graph_stats.o obj/cortex/bubble_find.o obj/cortex/report_output.o
 KMERINFO_OBJ =  obj/cortex/flags.o obj/cortex/path.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_table.o obj/cortex/file_reader.o obj/util/kmerinfo.o obj/cortex/logger.o obj/cortex/hash_value.o
 GRAPHOUT_OBJ = obj/cortex/flags.o obj/cortex/path.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_table.o obj/cortex/file_reader.o obj/cortex/dB_graph.o obj/util/graphout.o obj/cortex/perfect_path.o obj/cortex/logger.o obj/cortex/hash_value.o obj/util/graph_formats.o obj/util/node_queue.o obj/cortex/cleaning.o obj/cortex/coverage_walk.o obj/util/graph_tools.o obj/cortex/file_format.o
 FILTERREADS_OBJ = obj/util/filter_reads.o obj/cortex/flags.o obj/cortex/path.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_table.o obj/cortex/file_reader.o obj/cortex/dB_graph.o obj/cortex/perfect_path.o obj/cortex/logger.o obj/cortex/hash_value.o obj/util/node_queue.o obj/cortex/cleaning.o obj/cortex/file_format.o
@@ -123,29 +119,29 @@ HASH_TABLE_TESTS_OBJ = obj/cortex/flags.o obj/test/run_hash_table_tests.o obj/co
 GRAPH_TESTS_OBJ = obj/cortex/branches.o obj/cortex/file_format.o obj/test/test_dB_graph.o obj/cortex/logger.o  obj/cortex/cleaning.o  obj/cortex/perfect_path.o obj/cortex/path.o obj/cortex/flags.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_value.o obj/cortex/hash_table.o obj/cortex/dB_graph.o obj/cortex/file_reader.o obj/cortex/y_walk.o  obj/test/test_file_reader.o obj/test/test_graph_element.o obj/test/run_dB_graph_tests.o
 
 #Library objects
-LIBRARY_OBJ =  obj/cortex/file_format.o obj/cortex/analysis.o obj/cortex/flags.o obj/cortex/cleaning.o obj/cortex/path.o obj/cortex/perfect_path.o obj/cortex/branches.o obj/cortex/y_walk.o obj/cortex/cmd_line.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_value.o obj/cortex/hash_table.o obj/cortex/dB_graph.o obj/cortex/file_reader.o obj/cortex/metacortex.o obj/cortex/logger.o obj/cortex/metagraphs.o obj/cortex/coverage_walk.o obj/util/node_queue.o obj/cortex/graph_stats.o obj/cortex/bubble_find.o
+LIBRARY_OBJ =  obj/cortex/file_format.o obj/cortex/analysis.o obj/cortex/flags.o obj/cortex/cleaning.o obj/cortex/path.o obj/cortex/perfect_path.o obj/cortex/branches.o obj/cortex/y_walk.o obj/cortex/cmd_line.o obj/cortex/binary_kmer.o obj/cortex/seq.o obj/cortex/element.o obj/cortex/hash_value.o obj/cortex/hash_table.o obj/cortex/dB_graph.o obj/cortex/file_reader.o obj/cortex/metacortex.o obj/cortex/logger.o obj/cortex/metagraphs.o obj/cortex/coverage_walk.o obj/util/node_queue.o obj/cortex/graph_stats.o obj/cortex/bubble_find.o obj/cortex/report_output.o
 
 # Main rules
 metacortex : remove_objects $(METACORTEX_OBJ)
-	mkdir -p $(BIN); $(CC) -lm $(OPT) $(OPT_COLS) -o $(BIN)/metacortex_k$(BIN_SUFFIX) $(METACORTEX_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) $(OPT_COLS) -o $(BIN)/metacortex_k$(BIN_SUFFIX) $(METACORTEX_OBJ) -lm
 
 kmerinfo: remove_objects $(KMERINFO_OBJ)
-	mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/kmerinfo $(KMERINFO_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) -o $(BIN)/kmerinfo $(KMERINFO_OBJ) -lm
 
 graphout:remove_objects $(GRAPHOUT_OBJ)
-	mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/graphout_$(BIN_SUFFIX) $(GRAPHOUT_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) -o $(BIN)/graphout_$(BIN_SUFFIX) $(GRAPHOUT_OBJ) -lm
 
 filterreads:remove_objects $(FILTERREADS_OBJ)
-	mkdir -p $(BIN); $(CC) -lm $(OPT) -o $(BIN)/filterreads_$(BIN_SUFFIX) $(FILTERREADS_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) -o $(BIN)/filterreads_$(BIN_SUFFIX) $(FILTERREADS_OBJ) -lm
 
 run_basic_tests : remove_objects $(BASIC_TESTS_OBJ)
-	mkdir -p $(BIN); $(CC) $(OPT) $(CFLAGS_CUNIT) $(CFLAGS_BASIC_TESTS)      -lcunit -o $(BIN)/run_basic_tests_$(MAXK)$(READ_PAIR_SUFFIX) $(BASIC_TESTS_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) $(CFLAGS_CUNIT) $(CFLAGS_BASIC_TESTS)      -lcunit -o $(BIN)/run_basic_tests_$(BIN_SUFFIX)$(READ_PAIR_SUFFIX) $(BASIC_TESTS_OBJ)
 
 run_hash_table_tests : remove_objects $(HASH_TABLE_TESTS_OBJ)
-	mkdir -p $(BIN); $(CC) $(OPT) $(CFLAGS_CUNIT) $(CFLAGS_HASH_TABLE_TESTS) -lcunit -o $(BIN)/run_hash_table_tests_$(MAXK) $(HASH_TABLE_TESTS_OBJ)
+	mkdir -p $(BIN); $(CC) $(OPT) $(CFLAGS_CUNIT) $(CFLAGS_HASH_TABLE_TESTS) -lcunit -o $(BIN)/run_hash_table_tests_$(BIN_SUFFIX) $(HASH_TABLE_TESTS_OBJ)
 
 run_graph_tests : remove_objects $(GRAPH_TESTS_OBJ)
-	mkdir -p $(BIN); $(CC) $(LINKOPT) $(CFLAGS_CUNIT)  -o $(BIN)/run_graph_tests_$(MAXK) $(GRAPH_TESTS_OBJ) -lcunit
+	mkdir -p $(BIN); $(CC) $(LINKOPT) $(CFLAGS_CUNIT)  -o $(BIN)/run_graph_tests_$(BIN_SUFFIX) $(GRAPH_TESTS_OBJ) -lcunit
 
 tests: remove_objects run_basic_tests run_hash_table_tests run_graph_tests
 

diff --git a/README.md b/README.md
diff --git a/binders/ruby/Bio/Cortex.rb b/binders/ruby/Bio/Cortex.rb
diff --git a/binders/ruby/test.rb b/binders/ruby/test.rb
diff --git a/data/test/basic/long_entries.fasta b/data/test/basic/long_entries.fasta
diff --git a/data/test/basic/one_long_entry.fasta b/data/test/basic/one_long_entry.fasta
diff --git a/data/test/count_kmers/filelist_repeats_in_same_entry b/data/test/count_kmers/filelist_repeats_in_same_entry
diff --git a/data/test/graph/chrom1.fasta b/data/test/graph/chrom1.fasta
diff --git a/data/test/graph/chrom2.fasta b/data/test/graph/chrom2.fasta
diff --git a/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio.fasta b/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio.fasta
diff --git a/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person0.fasta b/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person0.fasta
diff --git a/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person1.fasta b/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person1.fasta
diff --git a/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person2 b/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person2
diff --git a/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person2.fasta b/data/test/graph/fasta_for_dumping_by_graph_and_reload_by_sv_trio_person2.fasta
diff --git a/data/test/graph/file_to_test_covg_of_reads.fasta b/data/test/graph/file_to_test_covg_of_reads.fasta
diff --git a/data/test/graph/filelist_fasta_to_load_and_dump_as_bin b/data/test/graph/filelist_fasta_to_load_and_dump_as_bin
diff --git a/data/test/graph/generate_bubble_with_unequal_branch_sizes.fa b/data/test/graph/generate_bubble_with_unequal_branch_sizes.fa
diff --git a/data/test/graph/list_paired_end_file3_left b/data/test/graph/list_paired_end_file3_left
diff --git a/data/test/graph/list_paired_end_file3_right b/data/test/graph/list_paired_end_file3_right
diff --git a/data/test/graph/long_entries.fasta b/data/test/graph/long_entries.fasta
diff --git a/data/test/graph/paired_end_file1_1.fastq b/data/test/graph/paired_end_file1_1.fastq
diff --git a/data/test/graph/paired_end_file1_2.fastq b/data/test/graph/paired_end_file1_2.fastq
diff --git a/data/test/graph/paired_end_file2_with_dup_1.fastq b/data/test/graph/paired_end_file2_with_dup_1.fastq
diff --git a/data/test/graph/paired_end_file2_with_dup_2.fastq b/data/test/graph/paired_end_file2_with_dup_2.fastq
diff --git a/data/test/graph/paired_end_file3_with_dups_1.fastq b/data/test/graph/paired_end_file3_with_dups_1.fastq
diff --git a/data/test/graph/paired_end_file3_with_dups_2.fastq b/data/test/graph/paired_end_file3_with_dups_2.fastq
diff --git a/data/test/graph/person.fasta b/data/test/graph/person.fasta
diff --git a/data/test/graph/person2.fasta b/data/test/graph/person2.fasta
diff --git a/data/test/graph/person3.fasta b/data/test/graph/person3.fasta
diff --git a/data/test/graph/person3_with_errors.fastq b/data/test/graph/person3_with_errors.fastq
diff --git a/data/test/graph/person3_with_errors_extended_file.fastq b/data/test/graph/person3_with_errors_extended_file.fastq
diff --git a/data/test/graph/person_with_deletion_in_chrom.fasta b/data/test/graph/person_with_deletion_in_chrom.fasta
diff --git a/data/test/graph/person_with_sv.fasta b/data/test/graph/person_with_sv.fasta
diff --git a/data/test/graph/test_db_graph_intermediate_output_file b/data/test/graph/test_db_graph_intermediate_output_file
diff --git a/data/test/read_pair/rp_1.fastq b/data/test/read_pair/rp_1.fastq
diff --git a/data/test/read_pair/rp_2.fastq b/data/test/read_pair/rp_2.fastq
diff --git a/data/test/read_pair/rp_test.txt b/data/test/read_pair/rp_test.txt
diff --git a/data/test/solid/simple_test.csfasta b/data/test/solid/simple_test.csfasta
diff --git a/data/test/solid/simple_test_two_reads.csfasta b/data/test/solid/simple_test_two_reads.csfasta
diff --git a/data/test/solid/simple_test_with_comment.csfasta b/data/test/solid/simple_test_with_comment.csfasta
diff --git a/data/test/solid/test1.txt b/data/test/solid/test1.txt
diff --git a/data/test/solid/test2.txt b/data/test/solid/test2.txt
diff --git a/data/test/solid/test3.txt b/data/test/solid/test3.txt
diff --git a/data/test/solid/test_one_sec_multiple_input.csfasta b/data/test/solid/test_one_sec_multiple_input.csfasta
diff --git a/data/test/solid/test_one_sec_multiple_input.fa b/data/test/solid/test_one_sec_multiple_input.fa
diff --git a/data/test/solid/test_one_seq_cs.fa b/data/test/solid/test_one_seq_cs.fa
diff --git a/data/test/solid/test_one_seq_cs.txt b/data/test/solid/test_one_seq_cs.txt
diff --git a/data/test/solid/test_two_sec_multiple_input.csfasta b/data/test/solid/test_two_sec_multiple_input.csfasta
diff --git a/data/test/solid/test_two_sec_multiple_input.fa b/data/test/solid/test_two_sec_multiple_input.fa
diff --git a/data/test/solid/test_two_secs_multiple_input.fa b/data/test/solid/test_two_secs_multiple_input.fa
diff --git a/degree_plots.R b/degree_plots.R
@@ -0,0 +1,93 @@
+library(ggplot2)
+library(scales)
+library(grid)
+
+
+#filename="/home/aylingm/testgenome/patronol/contigs_46_100k.1_clean.fa.degrees"
+#filename="/home/aylingm/testgenome/mc_consensus_3k/contigs.fa.degrees"
+
+cmd_args = commandArgs(TRUE);
+filename=cmd_args[1];
+#print(filename)
+
+format="png"
+# these need to be fixed! use dirname(), and check for directory existence, mkdir if not there
+graphsdir=paste(dirname(filename), "/graphs", sep="");
+if(!dir.exists(graphsdir)){
+  dir.create(graphsdir, showWarnings = TRUE, recursive = FALSE, mode = "0777")
+}
+
+#print(graphsdir)
+
+types = c("I", "Y", "X","E");
+min_graph=100 # need to have this as a variable that can be passed to the script
+scaling_factor=100
+bin_size=0.0001
+title_font=7
+decimal_points=4
+
+degrees <- read.delim(filename)
+if (min(degrees$total)<min_graph){
+  min_graph<-min(degrees$total)-1
+}
+degrees <- degrees[degrees$total>min_graph,]
+
+
+for (t in 1:4) {
+  x_high<-c(0.95,1)
+  x_low<-c(0,0.05)
+  type = types[t];
+  if (type=="I"){
+    Is<-data.frame(degrees$for.1.rev.1.)
+    degree_dist<-data.frame(Is)
+    x_min<-x_high[1]
+    x_max<-x_high[2]
+  }
+  else if (type=="Y"){
+    Ys<-data.frame(degrees$for.1.rev.2., degrees$for.1.rev.3., degrees$for.1.rev.4., degrees$for.2.rev.1., degrees$for.3.rev.1., degrees$for.4.rev.1.)
+    degree_dist<-data.frame(rowMeans(Ys))
+    x_min<-x_low[1]
+    x_max<-x_low[2]
+  }
+  else if (type=="X"){
+    Xs<-data.frame(degrees$for.1.rev.2., degrees$for.1.rev.3., degrees$for.1.rev.4., degrees$for.2.rev.1., degrees$for.3.rev.1., degrees$for.4.rev.1.,degrees$for.2.rev.2., degrees$for.2.rev.3., degrees$for.2.rev.4., degrees$for.3.rev.3., degrees$for.3.rev.2., degrees$for.3.rev.4., degrees$for.4.rev.4., degrees$for.4.rev.2., degrees$for.4.rev.3.)
+    degree_dist<-data.frame(rowMeans(Xs))
+    x_min<-x_low[1]
+    x_max<-x_low[2]
+  }
+  else if (type=="E"){
+    Es<-data.frame(degrees$for.0.rev.0., degrees$for.0.rev.1., degrees$for.0.rev.2., degrees$for.0.rev.3., degrees$for.0.rev.4., degrees$for.1.rev.0., degrees$for.2.rev.0., degrees$for.3.rev.0., degrees$for.4.rev.0.)
+    degree_dist<-data.frame(rowMeans(Es))
+    x_min<-x_low[1]
+    x_max<-x_low[2]
+  }
+
+  degrees_png <- paste(graphsdir, "/", type,"_degrees.png", sep="");
+  png(degrees_png, width=1200, height=800)
+  degree_dist<-degree_dist*scaling_factor
+  sd_dd<-sd(degree_dist[,1])
+  mean_dd<-mean(degree_dist[,1])
+  print(ggplot(degree_dist, aes(degree_dist)) + ggtitle(paste(type ,"nodes probability,", "mean=",round(mean_dd,decimal_points),"sd=",round(sd_dd,decimal_points))) + 
+          xlab("probability (%)") + ylab("Subgraph Count") + geom_histogram(binwidth=bin_size*scaling_factor) + 
+          scale_x_continuous(breaks=seq(0, 1*scaling_factor, bin_size*10*scaling_factor), limits=c(x_min*scaling_factor, x_max*scaling_factor))) +
+          theme(plot.title = element_text(size=title_font))
+  garbage <- dev.off()
+}
+
+type="E"
+degrees.not_meaned<-data.frame(degrees[degrees$total>min_graph,-26])
+degrees.m<-data.frame("FOR"=rep(c(0:4),each = 5),"REV"=rep(0:4,5), data.frame(colMeans(degrees[degrees$total>min_graph,-26]*scaling_factor))) # manually 'melt' the average for each point
+names(degrees.m)[3]<-"prob"
+degrees_png <- paste(graphsdir, "/", type,"_heatmap.png", sep="")
+png(degrees_png, width=1200, height=800)
+print(ggplot(degrees.m, aes(x=FOR, y=REV)) + geom_tile(aes(fill = prob), colour = "white") + ggtitle(paste(filename, "_", type,"_heatmap")) + theme(plot.title = element_text(size=title_font)) + scale_fill_gradient(low = "white", high = "steelblue", trans='log'))
+garbage <- dev.off()
+
+degrees.not_meaned<-data.frame(degrees[degrees$total>min_graph,-26])
+degrees.not_meaned$for.1.rev.1.<-0
+degrees.m<-data.frame("FOR"=rep(c(0:4),each = 5),"REV"=rep(0:4,5), data.frame(colMeans(degrees.not_meaned*scaling_factor))) # manually 'melt' the average for each point
+names(degrees.m)[3]<-"prob"
+degrees_png <- paste(graphsdir, "/", type,"_heatmap_noI.png", sep="")
+png(degrees_png, width=1200, height=800)
+print(ggplot(degrees.m, aes(x=FOR, y=REV)) + geom_tile(aes(fill = prob), colour = "white")+ ggtitle(paste(filename, "_", type,"_heatmap (ex. I nodes)")) + theme(plot.title = element_text(size=title_font))+ scale_fill_gradient(low = "white", high = "steelblue", trans='log'))
+garbage <- dev.off()
diff --git a/doc/metacortexmanual.pdf b/doc/metacortexmanual.pdf
diff --git a/doc/metacortexmanual.tex b/doc/metacortexmanual.tex
diff --git a/doc/typicalprocess.pdf b/doc/typicalprocess.pdf
diff --git a/gpl.txt b/gpl.txt