Nick's updates to v6.0

README

@@ -1,4 +1,4 @@
-ADMIXTOOLS version 5.1  9/18/18 (for Linux and Mac)
+ADMIXTOOLS version 6.0  1/10/20 (for Linux and Mac)
 
 See README.INSTALL for installation info. 
 
@@ -44,6 +44,21 @@ beyond our scope.
 Nick Patterson
 <[email protected]>
 
+*** NEW *** 
+Lightweight onlline documentation added, thanks to Eric Deveaud                             
+<executable>  or <executable> -h  to get brief documentation or
+
+*** NEW ***  
+Alter number of chromosomes:   
+numchrom:  <zzz>
+zzz should be the autosome number (default 22 -- the number for humans) 
+
+Custom block numbers (for jackknife) 
+blockname:  <bbb> 
+bbb should contain a list of snps 1 / line followed by a block number (integer) 
+block number should be at least 1.  -1 -> snp ignored.  If this option is used 
+snps not in list will be ignored. 
+
 ----------------------------
 SOFTWARE COPYRIGHT NOTICE AGREEMENT
 This software and its documentation are copyright (2010) by Harvard University 

README.Dstatistics

@@ -31,9 +31,10 @@ parfile: Name of parameter file
 
 NEW FEATURE
 In some cases using popfilename (see below) the program uses an excessive amount of memory.  
-A solution, designed to be convenient is to make multiple runs with -l lo -h hi set when only lines 
+A solution, designed to be convenient, is to make multiple runs with -L lo -H hi set when only lines 
 lo through hi (starting at 1) of popfilename will be used.  This makes it easy to do multiple runs 
 and then extract all results by grep result: ... 
+*** note new parameter flags.  Used to be -l, -h  
 
 DESCRIPTION OF EACH PARAMETER in parfile:
 

README.INSTALL

@@ -1,4 +1,4 @@
-ADMIXTOOLS version 5.1  9/18/18 (for Linux and Mac)
+ADMIXTOOLS version 5.0  6/28/18 (for Linux and Mac)
 
 Best is to recompile on your system. 
 

README.QPGRAPH

@@ -55,12 +55,12 @@ admix T S1 S2 w1 w2
 These lines are in the same format as the output graph [-o option below] and such a graph can be used 
  (only admix lines are recognized) 
 admixout:  <admixwts file> 
-This file is of course easy to habnd edit. 
+This file is of course easy to hand edit. 
 If admixin is present then initial try estimation is omitted which will make qpGraph run 
  very much faster.  
-
-
-
+inbreed:  YES 
+Genotypes are expected to be pseudo-haploid -- 2 samples at least per population or drift lengths on 
+leaves are not meaningful.  
 
 
 -g graph  

README.QpWave

@@ -22,7 +22,7 @@ logfile: Name of the logfile. The logfile contains the output of the run.
 parfile: Name of parameter file
 
 qpWave gives evidence of the number of admixture flows between the left and right populations,
- and should be run as a precursor to qpAdm (see below).
+ and should usually be run as a precursor to qpAdm (see below).
 
 DESCRIPTION OF EACH PARAMETER in parfile:
 
@@ -33,6 +33,13 @@ popleft:       left population list (1 per line)
 popright:      right population list (1 per line) 
 details:       YES 
 
+allsnps: YES
+## default NO 
+When set to YES, the maximum number of snps available for each f4 statistic are used. By default,
+only the intersect of snps across all Left and Right populations are used.
+
+chrom: Only use snps in the specified chromosome.
+
 DESCRIPTION OF OUTPUT FILE:
 The program will write all the output to stdout. The output file prints the parfile entered by the user, 
 number of snps and individuals, jackknife block size, number of blocks for jackknife and the results.

README.ROLLOFF

@@ -66,4 +66,10 @@ Nick Patterson
 ------------------------------------------------------------------------------
 Last revision: 2016-01-11
 
+-------------------------------------------------------------------------------------
+*** A new program DATES developed by the Moorjani lab seems superior to rolloff.  See 
+https://github.com/priyamoorjani/DATES  
+
+12/15/2019 
+
 

README.qp4diff

@@ -0,0 +1,56 @@
+DOCUMENTATION OF qp4diff:
+
+It is often useful to directly test the difference of 2 f4 statistics.  
+If we merely run qpDstat and difference 2 results, we cannot correctly compute standard errors. 
+
+qp4diff requires that the input data is available in one of the 5 supported formats. 
+
+
+Executable and source code:
+------------------------------------------------------------------------------
+
+For information about installing the program, see README.ADMIXTOOLS. After installing the programs, the executable qp4diff) should be located in the bin directory.
+
+To run qp4diff, type the following on a linux machine. 
+$DIR/bin/qp4diff -p parfile >logfile
+
+$DIR: Path to the bin directory.
+logfile: Name of the logfile. The logfile contains the output of the run. 
+parfile: Name of parameter file
+
+DESCRIPTION OF EACH PARAMETER in parfile:
+
+genotypename:   input genotype file (in eigenstrat format)
+snpname:   input snp file      (in eigenstrat format)
+indivname:   input indiv file    (in eigenstrat format)
+popfilename:  list (contains list of 8 populations- A B : C D :: E F : G H  
+Colon separators are not required and are ignored by the program. They have been included to make the input/output more readable). 
+Populations can repeat beteeen the left and right quadruplets 
+blgsize:	jackknife block size (in centimorgan)
+
+*** 2 optional parameters *** 
+allsnps:  YES   
+## default.  By default only SNPs with valid f4 for both quads are used.  
+firstf4mult:  val 
+The first f4 is multiplied by val.  Can be used to test if alpha a_1 = a_2 for a fixed alpha.  
+
+Note:
+If you would like to use SNP number to define block size, you can:
+make a fake .snp file with (false) physical positions, and 0 genetic distances.  
+The software defaults to 1M bases = 1cm, so if (for example) you set the
+distance between each snp as 10000 bases and blgsize: .01 then each block
+will be 100 snps.
+
+DESCRIPTION OF OUTPUT FILE:
+The program will write all the output to stdout. The output file prints the parfile entered by the user, number of snps and individuals, jackknife block size, number of blocks for jackknif
+e and the results.
+
+The results have the following format -
+result:  A B C D : E F G H  f4diff std. error Z  
+
+Nick Patterson
+<[email protected]>
+------------------------------------------------------------------------------
+
+
+

examples/README

@@ -0,0 +1,2 @@
+Download data directory from 
+ Reich Lab web page.  datasets :: Affymmetrix Human Origins (2012) 

src/Makefile

@@ -21,16 +21,19 @@ endif
 ND = nicksrc
 NLIB = $(ND)/libnick.a
 
-PROGS= qp3Pop qpDstat qpF4ratio qpAdm qpWave qp4diff dowtjack expfit.sh  qpBound qpGraph qpreroot qpff3base qpDpart convertf mergeit ##  gcount kimf
+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 
 
 all: $(NLIB) $(PROGS) 
 
+
 $(NLIB):
 	$(MAKE) -C $(ND)
 
+## an ubuntu user found he needed: make all LDLIBS="-llapack" 
+
 statsubs.o:     tables nicksrc/statsubs.c
 	$(CC)  $(CFLAGS) -o statsubs.o nicksrc/statsubs.c
 
@@ -106,7 +109,6 @@ rmdirs:
 
 qpGraph: $(NLIB) qpGraph.o gslqp.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
 
-qpgbug: $(NLIB) qpgbug.o gslqp.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o
 
 qpreroot: qpreroot.o qpgsubs.o qpsubs.o mcio.o ldsubs.o admutils.o egsubs.o regsubs.o