Merge branch 'devlp' version 1.25.

.gitignore

@@ -2,8 +2,8 @@
 *~
 core
 depend
+doc
 raf
-version.h
 xboot
 xdtnorm
 xexopar
@@ -19,6 +19,7 @@ xpopnode
 xpopnodetab
 xsampndx
 xsimsched
+xstate
 xstrtab
 xterm
 xbranchtab
@@ -29,11 +30,14 @@ xjobqueue
 xdafreader
 xrafreader
 xmisc
+xscrmreader
 xstrint
+joinraf
 legosim
 numcores
 legofit
 tabpat
+scrmpat
 sitepat
 tabpat.log
 daf

src/Makefile

@@ -1,14 +1,15 @@
 destination := $(HOME)/bin
 global_destination := $(HOME)/group/bin
 opt := -DNDEBUG -O3  -finline-functions  # For full optimization
-#opt :=  -O0 -fno-inline-functions -rdynamic -DDEBUG     # For debugging
+#opt := -O0 -fno-inline-functions -rdynamic -DDEBUG     # For debugging
 #opt := -O3  -finline-functions  # Optimization + debugging
 #prof := -pg -rdynamic                    # For profiling
 prof :=
 incl := -I/usr/local/include -I/opt/local/include
 
-targets := legosim legofit tabpat sitepat daf raf numcores
-pytargets := diverg.py bootci.py flatfile.py
+targets := legosim legofit tabpat sitepat scrmpat daf raf numcores joinraf \
+     raf2daf
+pytargets := diverg.py bootci.py flatfile.py axt2raf.py
 tests := xzeroin xbinary
 
 CC := gcc
@@ -43,9 +44,6 @@ test : $(tests)
 	-./xzeroin
 	@echo "ALL UNIT TESTS WERE COMPLETED."
 
-version.h:
-	./mkversion.py > version.h
-
 LEGOSIM := legosim.o patprob.o gptree.o binary.o jobqueue.o misc.o parse.o \
   branchtab.o popnodetab.o lblndx.o tokenizer.o parstore.o parkeyval.o \
   popnode.o gene.o dprintf.o rngseed.o dtnorm.o tinyexpr.o
@@ -55,7 +53,7 @@ legosim : $(LEGOSIM)
 LEGOFIT := legofit.o patprob.o gptree.o binary.o jobqueue.o misc.o \
   parse.o branchtab.o popnodetab.o lblndx.o tokenizer.o parstore.o \
   parkeyval.o popnode.o gene.o cost.o diffev.o dprintf.o rngseed.o \
-  simsched.o dtnorm.o tinyexpr.o
+  simsched.o dtnorm.o tinyexpr.o state.o
 legofit : $(LEGOFIT)
 	$(CC) $(CFLAGS) -o $@ $(LEGOFIT) $(lib)
 
@@ -69,6 +67,19 @@ SITEPAT := sitepat.o misc.o binary.o lblndx.o parkeyval.o rafreader.o \
 sitepat : $(SITEPAT)
 	$(CC) $(CFLAGS) -o $@ $(SITEPAT) $(lib)
 
+JOINRAF := joinraf.o rafreader.o error.o tokenizer.o misc.o
+joinraf : $(JOINRAF)
+	$(CC) $(CFLAGS) -o $@ $(JOINRAF) $(lib)
+
+RAF2DAF := raf2daf.o rafreader.o error.o tokenizer.o misc.o
+raf2daf : $(RAF2DAF)
+	$(CC) $(CFLAGS) -o $@ $(RAF2DAF) $(lib)
+
+SCRMPAT := scrmpat.o misc.o binary.o lblndx.o parkeyval.o scrmreader.o \
+  tokenizer.o boot.o error.o
+scrmpat : $(SCRMPAT)
+	$(CC) $(CFLAGS) -o $@ $(SCRMPAT) $(lib)
+
 DAF := daf.o misc.o
 daf : $(DAF)
 	$(CC) $(CFLAGS) -o $@ $(DAF) $(lib)
@@ -107,5 +118,4 @@ include depend
 
 .SUFFIXES:
 .SUFFIXES: .c .o
-.PHONY: clean
 

src/README.md

@@ -6,27 +6,29 @@ Legofit is a computer package that uses counts of nucleotide site
 patterns to estimate the history of population size, subdivision, and
 gene flow. The package consists of the following programs
 
-* @ref daf "daf", which writes genetic data into the ".daf" format,
+* @ref daf "daf" writes genetic data into the ".daf" format,
   which is used by @ref tabpat "tabpat".
-* @ref tabpat "tabpat", which reads ".daf" files for several
+* @ref tabpat "tabpat" reads ".daf" files for several
   populations, tabulates "nucleotide site patterns" (explained below),
   and generates moving-blocks bootstrap replicates.
-* @ref raf "raf", which writes genetic data into the ".raf" format,
+* @ref raf "raf" writes genetic data into the ".raf" format,
   which is used by @ref sitepat "sitepat".
-* @ref sitepat "sitepat", which reads ".raf" files for several
+* @ref sitepat "sitepat" reads ".raf" files for several
   populations, tabulates "nucleotide site patterns" (explained below),
   and generates moving-blocks bootstrap replicates.
-* @ref legosim "legosim", which predicts site pattern counts from
+* @ref scrmpat "scrmpat" tabulates site patterns from output generated
+  by the `scrm` coalescent simulator.
+* @ref legosim "legosim" predicts site pattern counts from
   assumptions about population history.
-* @ref legofit "legofit", which estimates parameters from site pattern
+* @ref legofit "legofit" estimates parameters from site pattern
   counts.
-* @ref bootci "bootci.py", which uses multiple legofit output files
+* @ref bootci "bootci.py" uses multiple legofit output files
   (one for the real data and one for each bootstrap replicate) to
   generate bootstrap confidence intervals for estimated parameters.
-* @ref flatfile "flatfile.py", which reads a list of legofit output
+* @ref flatfile "flatfile.py" reads a list of legofit output
   files and writes a flat file with a row for each legofit file and a
   column for each parameter.
-* @ref diverg "diverg.py", which compares two distributions of site
+* @ref diverg "diverg.py" compares two distributions of site
   pattern frequencies, using the Kullback-Leibler (KL) divergence.
 
 # Nucleotide site patterns {#sitepat}
@@ -453,6 +455,21 @@ format is described above. Then, you can execute `legosim` by typing:
 
 See the @ref legosim "legosim" documentation for details.
 
+## Simulating site patterns
+
+The preferred approach is to do simulations using
+[scrm](https://scrm.github.io/), a software package written by Paul
+R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter. It does coalescent
+simulations with linkage and recombination. Our own program @ref
+scrmpat "scrmpat" tabulates site pattern frequencies from `scrm`
+output.
+
+For less sophisticated simulations, use the `-U` option of @ref
+legosim "legosim". This assumes free recombination between nucleotide
+sites. This is not ideal, because it ignores genetic linkage, but it
+reads the same input files as `legosim`, is very fast, and generates
+output in the form of site pattern frequencies.
+
 ## Estimating parameters from genetic data
 
 This involves several programs. The first step is to generate input