merged nick's changes

README

@@ -1,4 +1,4 @@
-EIGENSOFT version 6.1.4, 9/2/16 (for Linux only)
+EIGENSOFT version 6.1.4, 9/7/16 (for Linux only)
 
 The EIGENSOFT package implements methods from the following 3 papers:
 Patterson et al. 2006 PLoS Genet (population structure)
@@ -7,8 +7,11 @@ Galinsky et al. 2016 Am J Hum Genet (FastPCA and PC-based selection statistic)
 
 NEW features of EIGENSOFT version 6.1.4 include:
 -- pcaselection was omitted from 6.1.3 by accident
--- statically linked GSL/openblas
--- fixed memory allocation bug in pcaselection
+-- Statically linked GSL/openblas
+-- Fixed memory allocation bug in pcaselection
+-- Some routines moved into nicklib
+-- Error message on allocate failure now prints length as "%ld"
+   supporting long values.
 
 NEW features of EIGENSOFT version 6.1.3 include:
 -- Restored script file extensions to .perl instead of .pl

include/egsubs.h

@@ -1,14 +1,10 @@
-#include "admutils.h"  
+#include "admutils.h"
 
-int
-makeeglist (char **eglist, int maxnumeg, Indiv **indivmarkers, int numindivs);
-int
-mkeglist (Indiv **indm, int numindivs, char **eglist);
-void
-seteglist (Indiv **indm, int nindiv, char *eglistname);
-void
-seteglistv (Indiv **indm, int nindiv, char *eglistname, int val);
-int
-loadlist (char **list, char *listname);
-int
-loadlist_type (char **list, char *listname, int *ztypes, int off);
+
+int makeeglist (char **eglist, int maxnumeg, Indiv ** indivmarkers,
+		int numindivs);
+int mkeglist (Indiv ** indm, int numindivs, char **eglist);
+void seteglist (Indiv ** indm, int nindiv, char *eglistname);
+void seteglistv (Indiv ** indm, int nindiv, char *eglistname, int val);
+int loadlist (char **list, char *listname);
+int loadlist_type (char **list, char *listname, int *ztypes, int off);

include/strsubs.h

@@ -1,142 +1,87 @@
 #include <stdlib.h>
 
-int
-splitup (char *strin, char *strpt[], int maxpt);
-int
-splitupx (char *strin, char **spt, int maxpt, char splitc);
-int
-splitupwxbuff (char *strin, char **spt, int maxpt, char *bigbuff,
-               int bigbufflen);
-int
-splitupxbuff (char *strin, char **spt, int maxpt, char splitc, char *bigbuff,
-              int bigbufflen);
-int
-oldsplitup (char *strin, char *strpt[], int maxpt);
-void
-freeup (char *strpt[], int numpt);
-int
-split1 (char *strin, char *strpt[], char splitc);
-int
-first_word (char *string, char *word, char *rest);
-char *
-fnwhite (char *ss);
-char *
-fwhite (char *ss);
-char *
-ftab (char *ss);
-int
-NPisnumber (char c);
-int
-isnumword (char *str);
-void
-fatalx (char *fmt, ...);
-long
-seednum ();
-void
-printbl (int n);
-void
-printnl ();
-void
-striptrail (char *sss, char c);
-void
-catx (char *sout, char **spt, int n);
-void
-catxx (char *sout, char **spt, int n);
-void
-catxc (char *sout, char **spt, int n, char c);
-void
-makedfn (char *dirname, char *fname, char *outname, int maxstr);
-int
-substring (char **ap, char *inx, char *outx);
-int
-numcols (char *name);
-int
-numlines (char *name);
-void
-openit (char *name, FILE **fff, char *type);
-int
-ftest (char *aname);
-int
-getxx (double **xx, int maxrow, int numcol, char *fname);
-int
-getss (char **ss, char *fname);
-double
-clocktime ();  // cpu time in seconds
-void
-crevcomp (char *sout, char *sin);
-int
-indxstring (char **namelist, int len, char *strid);
-int
-indxstringr (char **namelist, int len, char *strid);
-char *
-strstrx (char *s1, char *s2);  // case insensitive strstr
-int
-getxxnames (char ***pnames, double **xx, int maxrow, int numcol, char *fname);
-int
-getjjnames (char ***pnames, int **xx, int maxrow, int numcol, char *fname);
-int
-getxxnamesf (char ***pnames, double **xx, int maxrow, int numcol, FILE *fff);
-int
-getnameslohi (char ****pnames, int maxrow, int numcol, char *fname, int lo,
-              int hi);
-int
-getnames (char ****pnames, int maxrow, int numcol, char *fname);
-char
-num2iub (int num);
-char
-revchar (char c);
-int
-iub2num (char c);
-char
-num2base (int num);
-int
-base2num (char c);
-char *
-int_string (int a, int len, int base);
-char *
-binary_string (int a, int len);
-int
-string_binary (char *sx);
-void
-freestring (char **ss);
-void
-copystrings (char **sa, char **sb, int n);
-void
-printstringsw (char **ss, int n, int slen, int width);
-void
-printstrings (char **ss, int n);
-int
-ridfile (char *fname);
-char
-compbase (char x);
-void
-mkupper (char *sx);
-void
-mklower (char *sx);
-int
-iubdekode (char *a, char iub);
-int
-isiub (char iub);
-int
-isiub2 (char iub);
-int
-iubcbases (char *cbases, char iub);
-int
-ishet (char c);
-int
-char2int (char cc);
-char
-int2char (int x);
-void
-chomp (char *str);
+int splitup (char *strin,  char *strpt[],int maxpt) ;
+int splitupx(char *strin, char **spt, int maxpt, char splitc)  ;
+int splitupwxbuff(char *strin, char **spt, int maxpt, char *bigbuff, int bigbufflen)  ;
+int splitupxbuff(char *strin, char **spt, int maxpt, char splitc, char *bigbuff, int bigbufflen)  ;
+int oldsplitup (char *strin,  char *strpt[],int maxpt) ;
+void freeup (char *strpt[],int numpt) ;
+int split1 (char *strin,  char *strpt[], char splitc);
+int first_word(char *string, char *word, char *rest) ;
+char *fnwhite (char *ss) ;
+char *fwhite (char *ss) ;
+char *ftab (char *ss) ;
+int NPisnumber (char c) ;
+int isnumword (char *str)  ;
+void fatalx( char *fmt, ...) ;
+long seednum() ;
+void printbl(int n) ;
+void printnl() ;
+void striptrail(char *sss, char c) ;
+void catx(char *sout, char **spt, int n) ;
+void catxx(char *sout, char **spt, int n) ;
+void catxc(char *sout, char **spt, int n, char c) ;
+void makedfn(char *dirname, char *fname, char *outname, int maxstr) ;
+int substring (char **ap, char *inx, char *outx) ;
+int numcols (char *name) ;
+int numlines(char *name) ;
+void openit(char *name, FILE **fff, char *type)  ;
+int  ftest(char *aname) ;
+int getxx(double **xx, int maxrow, int numcol, char *fname) ;
+int getss(char  **ss, char *fname) ;
+int  loadlist(char **list, char *listname)    ;  // with dup check
+void printdups(char **list, int n)  ;
+int checkdup(char **list, int n)  ;
+double clocktime() ;  // cpu time in seconds
+void crevcomp(char *sout, char *sin)  ;  
+int indxstring(char **namelist, int len, char *strid)  ;
+int indxstringr(char **namelist, int len, char *strid)  ;
+char *strstrx(char *s1, char *s2)  ;  // case insensitive strstr
+int getxxnames(char ***pnames, double **xx, int maxrow, int numcol, char *fname);
+int getjjnames(char ***pnames, int **xx, int maxrow, int numcol, char *fname);
+int getxxnamesf(char ***pnames, double **xx, int maxrow, int numcol, FILE *fff) ;
+int getnameslohi(char ****pnames, int maxrow, int numcol, char *fname, int lo, int hi) ;
+int getnamesstripcolon(char ****pnames, int maxrow, int numcol, char *fname, int lo, int hi) ;
+int getnames(char ****pnames, int maxrow, int numcol, char *fname) ;
+char num2iub (int num) ; 
+char revchar(char c) ;
+int  iub2num(char c) ;
+char num2base (int num) ; 
+int base2num(char c) ;
+char *int_string(int a, int len, int base) ;
+char *binary_string(int a, int len) ;
+int string_binary(char *sx) ;
+void freestring (char **ss) ;
+void copystrings(char **sa, char **sb, int n) ;
+void printstringsw(char **ss, int n, int slen, int width)  ;
+void printstrings(char **ss, int n)  ;
+int ridfile(char *fname) ; 
+char compbase(char x) ;
+void mkupper(char *sx) ;
+void mklower(char *sx) ;
+int iubdekode(char *a, char iub) ;  
+int isiub(char iub) ;  
+int isiub2(char iub) ;  
+int iubcbases(char *cbases, char iub) ;
+int ishet(char c) ;
+int cttype(char cc) ;
+int char2int(char cc) ;
+char int2char(int x) ;
+void chomp(char *str) ;
+
+int numcmatch(char *cc, int len, char c) ;
+int numcnomatch(char *cc, int len, char c) ;
+char *strnotchar(char *s, char c) ;
+char *findupper(char *s) ;
+char *fgetstrap(char *buff, int maxlen, FILE *fff, int *ret)  ;
+char readtonl(FILE *fff) ; 
+int  filehash(char *name) ;
+
+
 
-int
-numcmatch (char *cc, int len, char c);
-int
-numcnomatch (char *cc, int len, char c);
 
 #define ZALLOC(item,n,type)      if ((item = (type *)calloc((n),sizeof(type))) == NULL) \
-                                        fatalx("Unable to allocate %d unit(s) for item \n",n)
+                                        fatalx("Unable to allocate %ld unit(s) for item \n", (long) n)
 
 #undef MAX
 #undef MIN