Some minor bugfixes and an upgrade that Stephan Schiffels asked for

.gitignore

@@ -29,6 +29,7 @@ src/oldmakefile
 src/q1
 src/qaz
 src/qp3Pop
+src/qp4diff
 src/qpAdm
 src/qpBound
 src/qpDpart
@@ -39,7 +40,6 @@ src/qpGraph
 src/qpWave
 src/qpreroot
 src/rolloff
-src/rolloffp
 src/tables
 pdoc.aux
 pdoc.dvi

README.3PopTest

@@ -30,6 +30,15 @@ popfilename:  list_qp3test (contains 3 populations on each line <Source1 (A)> <S
 inbreed: YES  
 ## Use if target pop is inbred OR (and crucially) if target is pseudo-diploid
 
+*** NEW *** 
+By default f_3 output is normalized by estimatated heterozygosity 
+of the target.   This doesn't work if the target has no hets as can 
+happen in "outgroup f_3" mode.  In this case set:
+outgroupmode: YES
+when the f-3 denominator is set to an arbitrary .001
+
+
+
 
 DESCRIPTION OF OUTPUT FILE:
 The program will write all the output to stdout. The output file prints the parfile entered by the user, the number of populations included in the popfilename (nplist), the number of blocks for block jackknife, the number of snps included in the run and the results.

src/Makefile

@@ -21,7 +21,7 @@ endif
 ND = nicksrc
 NLIB = $(ND)/libnick.a
 
-PROGS= qp3Pop qpDstat qpF4ratio qpAdm qpWave dowtjack expfit.sh qpBound qpGraph qpreroot qpff3base qpDpart qp4diff qpF4ratio qpgbug grabpars rolloff rolloffp convertf mergeit
+PROGS= qp3Pop qpDstat qpF4ratio qpAdm qpWave qp4diff dowtjack expfit.sh  qpBound qpGraph qpreroot qpff3base qpDpart ##  gcount kimf
 ## rolloff* convertf mergeit from .../o2src
 
 PROGS2 = rexpfit.r  wtjack.pl 
@@ -48,6 +48,10 @@ qp4diff: $(NLIB) qp4diff.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.
 
 qpF4ratio: $(NLIB) qpF4ratio.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
 
+qpF4ratio: $(NLIB) qpF4ratio.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
+
+qpf4diff: $(NLIB) f4diff.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
+
 rolloff: $(NLIB) rolloff.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
 
 rolloffp: $(NLIB) rolloffp.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
@@ -106,3 +110,7 @@ qpgbug: $(NLIB) qpgbug.o gslqp.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o e
 
 qpreroot: qpreroot.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
 
+gcount: gcount.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
+
+kimf: kimf.o gslkim.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
+