Small updates to Makefile and README

 - lstdc++fs linking depends on GCC/LLVM versions (linking is still
   required even though it's in the standard C++17 library for old
   versions)
 - added `make install` command, placing vcfdist in INSTALLDIR
   (/usr/local/bin)
 - updated README
 - updated demo (THRESHOLD column, ../src/vcfdist -> vcfdist)

README.md

@@ -65,13 +65,14 @@ vcfdist is developed for Linux and its only dependencies are GCC v8+ and HTSlib.
 > sudo make install
 > export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 ```
-If you do already have HTSlib installed elsewhere, make sure you've added it to your `LD_LIBRARY_PATH`. At this point, installation is as simple as cloning the repository and building the executable. It should compile in less than one minute.
+If you do already have HTSlib installed elsewhere, make sure you've added it to your `LD_LIBRARY_PATH`, and that the HTSlib headers are included during compilation. At this point, installation is as simple as cloning the repository and building the executable. It should compile in less than one minute.
 
 ```bash
 > git clone https://github.com/timd1/vcfdist
 > cd vcfdist/src
 > make
-> ./vcfdist --version
+> sudo make install
+> vcfdist --version
 vcfdist v2.3.2
 ```
 
@@ -86,7 +87,7 @@ sudo docker run -it timd1/vcfdist:latest vcfdist --help
 
 The <a href="./demo">`demo`</a> directory contains a <a href="./demo/demo.sh">demo script</a> (shown below) and all required inputs. It operates on the first 5 million bases on `chr1`, and should run in about 3 seconds.
 ```bash
-../src/vcfdist \
+vcfdist \
     query.vcf \
     nist-v4.2.1_chr1_5Mb.vcf.gz \
     GRCh38_chr1_5Mb.fa \
@@ -100,7 +101,7 @@ You can expect to see <a href="./demo/output.txt">this output</a>.
 To include more details on intermediate results, run it again at higher verbosity by removing the `-v 0` flag.
 Please note that your results may not be identical, since vcfdist is under active development and handling of edge-cases may differ between versions.
 
-Please see additional options documented <a href="./src/README.md">here</a>, or run `./vcfdist --help`.
+Please see additional options documented <a href="./src/README.md">here</a>, or run `vcfdist --help`.
 
 The output TSV files are documented <a href="./docs/outputs.md">here</a>.
 

demo/demo.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 echo -e "Running vcfdist..."
-../src/vcfdist \
+vcfdist \
     query.vcf \
     nist-v4.2.1_chr1_5Mb.vcf.gz \
     GRCh38_chr1_5Mb.fa \

demo/output.txt

@@ -1,13 +1,13 @@
 PRECISION-RECALL SUMMARY
 
 TYPE	MIN_QUAL	TRUTH_TP	QUERY_TP	TRUTH_FN	QUERY_FP	PREC		RECALL		F1_SCORE	F1_QSCORE
-SNP	Q >= 0		8222            8222            1               2               0.999757	0.999878	0.999818	37.388565
-SNP	Q >= 0		8222            8222            1               2               0.999757	0.999878	0.999818	37.388565
+SNP	NONE Q >= 0	8222            8222            1               2               0.999757	0.999878	0.999818	37.388565
+SNP	BEST Q >= 0	8222            8222            1               2               0.999757	0.999878	0.999818	37.388565
 
 TYPE	MIN_QUAL	TRUTH_TP	QUERY_TP	TRUTH_FN	QUERY_FP	PREC		RECALL		F1_SCORE	F1_QSCORE
-INDEL	Q >= 0		876             876             51              12              0.986486	0.944984	0.965289	14.595358
-INDEL	Q >= 0		876             876             51              12              0.986486	0.944984	0.965289	14.595358
+INDEL	NONE Q >= 0	876             876             51              12              0.986486	0.944984	0.965289	14.595358
+INDEL	BEST Q >= 0	876             876             51              12              0.986486	0.944984	0.965289	14.595358
 
 TYPE	MIN_QUAL	TRUTH_TP	QUERY_TP	TRUTH_FN	QUERY_FP	PREC		RECALL		F1_SCORE	F1_QSCORE
-SV      Q >= 0          0               0               0               0               1.000000        1.000000        1.000000        100.000000
-SV      Q >= 0          0               0               0               0               1.000000        1.000000        1.000000        100.000000
+SV      NONE Q >= 0     0               0               0               0               1.000000        1.000000        1.000000        100.000000
+SV      BEST Q >= 0     0               0               0               0               1.000000        1.000000        1.000000        100.000000

src/Makefile

@@ -2,10 +2,18 @@ CXX = g++
 CXXFLAGS = -Wall -Wextra -std=c++17 -O3
 OBJS = globals.o print.o variant.o dist.o bed.o cluster.o phase.o edit.o timer.o
 TARGET = vcfdist
-LDLIBS = -lz -lhts -lstdc++fs -lpthread
+INSTALLDIR = /usr/local/bin
+
+LDLIBS = -lz -lhts -lpthread
+# g++ < 9.1 and llvm < 9.0 require linking to lstdc++fs
+# if using g++ >= 9.1 or llvm >= 9.0, please comment the following line
+LDLIBS += -lstdc++fs
 
 all: $(TARGET)
 
+install:
+	cp $(TARGET) $(INSTALLDIR)
+
 $(TARGET): $(OBJS) main.cpp
 	$(CXX) $(CXXFLAGS) $(OBJS) -o $(TARGET) main.cpp $(LDLIBS)