README version 7.0.2. Remove extraneous files.

README

@@ -1,10 +1,14 @@
-ADMIXTOOLS version 7.0  6/24/20 (for Linux and Mac)
+ADMIXTOOLS version 7.0.2  6/22/21 (for Linux and Mac)
 
 See README.INSTALL for installation info. 
 
 The ADMIXTOOLS package implements 5 methods described in 
 Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper.
 
+A user guide for qpAdm is now available in the supplementary materials for "Assessing the Performance of qpAdm:  A Statistical Tool for Studying Population Admixture" by Harney et al. (2020). 
+https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Harney_et_al_2020/13403225?file=26425355
+https://doi.org/10.25386/genetics.13403225.v2
+
 The package contains 6 programs: 
 convertf: See README.CONVERTF for documentation of programs for converting file formats.
 qp3Pop: See README.3PopTest for details of running f_3 test. This test can be used as a format test of admixture with 3 populations.
@@ -26,9 +30,25 @@ recompile the programs, type
 
 If you are building on a Mac, you will need gsl and openblas installed. 
 "brew install gsl"
-"brew install homebrew/science/openblas"
+"brew install openblas"
 Uncomment the lines in src/Makefile that modify the CFLAGS and LDFLAGS. 
 
+If these packages are not in standard directories, you can specify the 
+appropriate include and library directories with the CFLAGS and LDFLAGS 
+make variables. 
+For example, on the Harvard Medical School O2 cluster, the command is:
+'make CFLAGS="-I/n/app/openblas/0.2.19/include -I/n/app/gsl/2.3/include" LDFLAGS="-L/n/app/openblas/0.2.19/lib -L/n/app/gsl/2.3/lib/"'
+On Mac OSX:
+'make CFLAGS="-I/usr/local/opt/openblas/include -I/usr/local/opt/gsl/include" LDFLAGS="-L/usr/local/opt/openblas/lib -L/usr/local/opt/gsl/lib"'
+
+If you have issues with missing lapacke symbols, for example "undefined reference to `LAPACKE_dlange'", run make with the corresponding additional libraries linked:
+'make LDLIBS="-llapacke"' on Linux Mint 18. 
+Similarly for Ubuntu, for "undefined reference to dspev_"
+'make LDLIBS="-llapack"'
+
+For questions about building this software: 
+Matthew Mah <matthew_mah@hms.harvard.edu>
+
 If you have trouble compiling and running our code, try compiling and
 running the examples in the examples/ directory. Download the example
 datasets from https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
@@ -45,24 +65,28 @@ Nick Patterson
 <nickp@broadinstitute.org>
 
 
-*** NEW *** 
-1) 
-Users of ADMIXTOOLS should know that an alternate version in R (native mode -- reimplementation) 
-written by Robert Maier is also available on Github.  
-See <https://github.com/uqrmaie1/admixtools> 
-Executables run fast, and it has features not available in this C version, such as interactive 
- exploration of graph phylogenies.
-
-2) 
-version 7.0 has numerous upgrades. 
-a) Two new executables --qpfstats qpfmv allow precomputation of f-statistic basis.  
-This can greatly reduce computation costs.  
-b) qpAdm, qpWave, qpGraph support qpfstats output as input.  
-*** This is a much improved way of running with allsnps: YES.    *** 
-c)  A new experimental feature of qpGraph (halfscore: YES) allows 
- comparison of 2 phylogenies + a (weak) goodness of fit score.  Be careful 
- if running with a large nnumber of populations and consider reducing block size say 
- blgsize: .005 
+*** NEW ***
+1)
+version 7.0 has numerous upgrades.
+a) Two new executables --qpfstats qpfmv allow precomputation of f-statistic basis.
+This can greatly reduce computation costs.
+b) qpAdm, qpWave, qpGraph support qpfstats output as input.
+*** This is a much improved way of running with allsnps: YES.    ***
+c)  A new experimental feature of qpGraph (halfscore: YES) allows
+ comparison of 2 phylogenies + a (weak) goodness of fit score.  Be careful
+ if running with a large number of populations and consider reducing block size say
+ blgsize: .005
+
+Version 7.0.2 has important bugfixes to qpfstats.  See README.qpfstats  
+
+2)
+Note that several of the new ideas implemented in version 7.0 were developed collaboratively with Robert Maier, who has implemented them along with the great majority of other ADMIXTOOLS functionality in R:
+See https://github.com/uqrmaie1/admixtools
+Executables run fast, and it has features not available in this C version, such as interactive exploration of graph phylogenies.
+A manuscript describing the algorithmic ideas and providing documentation of the methods is in preparation.
+
+
+
 
 
 *** Fairly NEW *** 

src/.gitignore

@@ -1 +1,38 @@
+backup
+convertf
+copych
+diff.out
+diffch
+dirlist
+dowtjack
 expfit.sh
+gcount
+gmon.out
+grabpars
+kimf
+libnick.a
+mergeit
+nicktmp
+oldmake
+oldmakefile
+q1
+qaz
+qp3Pop
+qp4diff
+qpAdm
+qpBound
+qpDpart
+qpdslow
+qpDstat
+qpff3base
+qpfmv
+qpfstats
+qpF4ratio
+qpGraph
+qpWave
+qpreroot
+rolloff
+rolloffp
+simpjack2
+tables
+qpmix