File List

Here is a list of all documented files with brief descriptions:

axt2raf.py
bepe.c
binary.c	Functions for fiddling with bits
binary.h
booma.c
boot.c	Functions for a moving blocks bootstrap
boot.h	Header for boot.c
bootci.py
branchtab.c	Hash table associating key (an unsigned int encoding a site pattern) and value (a double representing the length of the ascending branch)
branchtab.h
clic.c
comb.c	Combinations
comb.h
cost.c
cost.h
daf.c
dafreader.c	Class DAFReader: read a daf file
dafreader.h
diffev.c
diffev.h
diverg.py
dprintf.c	Define external mutex for locking output
dprintf.h
dtnorm.c	Pseudorandom numbers from a truncated Gaussian distribution
dtnorm.h
dtnorm_data.h
error.h
eventlst.h
flatfile.py
flatpat.py
gene.c	Class Gene
gene.h
gptree.c	Methods for simulating gene genealogies within a given tree of populations, and allowing populations to mix and also to split
gptree.h
hashmap.h
hessian.h
idset.c	A set of tipID_t values
idset.h
idsetset.c	A table of IdSet values
idsetset.h
intpart.c	Partitions of an integer into a given number of summands
intpart.h
jobqueue.c	Multithreaded job queue
jobqueue.h	Header for jobqueue.c
joinraf.c
lblndx.c	An index of sample labels
lblndx.h
legofit.c
legosim.c
linereader.h
longvec.c
longvec.h
mapmix.c
matcoal.h
mctree.h
misc.c	Functions that didn't seem to belong anywhere else
misc.h
mkfitted.c
mpfrmatcoal.h
ms2sim.c
network.c	Models a network of populations
network.h
param.h
parse.c	Parse a .lgo file
parse.h
parseopf.c	Parse a .opf file, containing site pattern frequencies
parseopf.h
parstore.c	Manage a vector of parameters
parstore.h
patprob.c	Calculate site pattern probabilities
patprob.h
pclgo.c
pointbuff.c	Class PointBuff
pointbuff.h
popnode.c	A single segment of a population tree
popnode.h
pripos.c
ptrlst.c
ptrlst.h
ptrptrmap.c	Map pointer to pointer
ptrptrmap.h
ptrqueue.c	A FIFO queue of pointers
ptrqueue.h
ptru32map.c	Map pointer to unsigned int
ptru32map.h
ptrvec.c
ptrvec.h
raf.c
raf2daf.c
rafdaf.c
rafreader.c	Class RAFReader: read a raf file
rafreader.h
rational.c
rational.h
resid.c
rngseed.c	Maintain seed of random number generator
sampndx.c	An index of haploid genetic samples
sampndx.h
scrmpat.c
scrmreader.c
scrmreader.h
segment.c	A single segment of a population tree
segment.h
setpart.h
simpat.c
simreader.c
simreader.h
simsched.c	Simulation schedule
simsched.h
sitepat.c
state.c	Read and write "state files", which describe the state of the optmizer
state.h
strdblmap.c	Map char* to double
strdblmap.h
strdblqueue.c	Functions for Composite Likelihood Information Criterion
strdblqueue.h
strint.c	Associate character strings with integers
strint.h
strptrmap.c	Map strings to pointers
strptrmap.h
strstrmap.c	Map char* to double
strstrmap.h
tabpat.c
tinyexpr.h
tokenizer.c	Tokenize a character string
tokenizer.h	Header for tokenizer.c
typedefs.h
u64i64map.c	Map uint64_t to int64_t
u64i64map.h
u64u64map.c	Map uint64_t to uint64_t
u64u64map.h
uintqueue.c	A FIFO queue of unsigned integers
uintqueue.h