From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: fsom is not used
--- libvcflib.orig/Makefile
+++ libvcflib/Makefile
@@ -114,9 +114,6 @@
 			  src/vcfnull2ref.cpp \
 			  src/vcfinfosummarize.cpp
 
-# when we can figure out how to build on mac
-# src/vcfsom.cpp
-
 #BINS = $(BIN_SOURCES:.cpp=)
 BINS = $(addprefix $(BIN_DIR)/,$(notdir $(BIN_SOURCES:.cpp=)))
 SHORTBINS = $(notdir $(BIN_SOURCES:.cpp=))
@@ -128,7 +125,6 @@
 INDELALLELE = smithwaterman/IndelAllele.o
 DISORDER = smithwaterman/disorder.o
 LEFTALIGN = smithwaterman/LeftAlign.o
-FSOM = fsom/fsom.o
 FILEVERCMP = filevercmp/filevercmp.o
 
 # Work out how to find htslib
@@ -194,9 +190,6 @@
 $(FASTAHACK): pre
 	cd fastahack && $(MAKE) && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) Fasta.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/
 
-#$(FSOM):
-#	cd fsom && $(CXX) $(CXXFLAGS) -c fsom.c -lm
-
 $(FILEVERCMP): pre
 	cd filevercmp && make && $(CP) *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && $(CP) *.o $(VCF_LIB_LOCAL)/$(INC_DIR)/
 
@@ -238,7 +231,6 @@
 	$(MAKE) clean -C smithwaterman
 	$(MAKE) clean -C fastahack
 	$(MAKE) clean -C multichoose
-	$(MAKE) clean -C fsom
 	$(MAKE) clean -C libVCFH
 	$(MAKE) clean -C test
 	$(MAKE) clean -C filevercmp
--- libvcflib.orig/README.md
+++ libvcflib/README.md
@@ -116,7 +116,6 @@
  * Generate potential **primers** from VCF records ([vcfprimers](#vcfprimers)), to check for genome uniqueness.
  * Convert the numerical represenation of genotypes provided by the GT field to a **human-readable genotype format** ([vcfgenotypes](#vcfgenotypes)).
  * Observe how different alignment parameters, including context and entropy-dependent ones, influence **variant classification and interpretation** ([vcfremap](#vcfremap)).
- * **Classify variants** by annotations in the INFO field using a self-organizing map ([vcfsom](#vcfsom)); **re-estimate their quality** given known variants.
 
 
 A number of "helper" perl and python3 scripts (e.g. vcf2bed.py, vcfbiallelic) further extend functionality.
@@ -571,47 +570,6 @@
 Prints the names of the samples in the VCF file.
 
     
-### vcfsom
-    
-    usage: vcfsom [options] [vcf file]
-    
-    training: 
-        vcfsom -s output.som -f "AF DP ABP" training.vcf
-    
-    application: 
-        vcfsom -a output.som -f "AF DP ABP" test.vcf >results.vcf
-    
-vcfsom trains and/or applies a self-organizing map to the input VCF data on stdin, adding two columns for the x and y coordinates of the winning neuron in the network and an optional euclidean distance from a given node (--center).
-    
-If a map is provided via --apply,  map will be applied to input without training.
-Automated filtering to an estimated FP rate is 
-    
-    options:
-    
-        -h, --help             this dialog
-    
-    training:
-    
-        -f, --fields "FIELD ..."  INFO fields to provide to the SOM
-        -a, --apply FILE       apply the saved map to input data to FILE
-        -s, --save  FILE       train on input data and save the map to FILE
-        -t, --print-training-results
-                               print results of SOM on training input
-                               (you can also just use --apply on the same input)
-        -x, --width X          width in columns of the output array
-        -y, --height Y         height in columns of the output array
-        -i, --iterations N     number of training iterations or epochs
-        -d, --debug            print timing information
-    
-    recalibration:
-    
-        -c, --center X,Y       annotate with euclidean distance from center
-        -p, --paint-true VCF   use VCF file to annotate true variants (multiple)
-        -f, --paint-false VCF  use VCF file to annotate false variants (multiple)
-        -R, --paint-tag TAG    provide estimated FDR% in TAG in variant INFO
-        -N, --false-negative   replace FDR% (false detection) with FNR% (false negative)
-    
-    
 ### vcfstats
     
     usage: vcfstats [options] <vcf file>
