ChangeLog

2009-01-23 16:42  kevin

	* Makefile.in, aclocal.m4, configure, configure.in, depcomp,
	  src/Makefile.am, src/Makefile.in, src/compute_classes.hpp: update
	  to make package 0.7.2

2009-01-23 16:41  kevin

	* src/MKtest.cc: added #include <limits>

2008-08-21 09:02  kevin

	* aclocal.m4, configure, configure.in: package 0.7.1

2008-08-21 09:02  kevin

	* src/compute_classes.cc: changed declaration of "arg history" to
	  "Sequence::arg history" to fix an issue with compiling on OS X.

2008-01-22 09:46  kevin

	* aclocal.m4, configure, configure.in: package 0.7.0

2008-01-22 09:45  kevin

	* src/: HBKpermute.cc, Makefile.am, Makefile.in, compute.cc,
	  descPoly.cc, distance.cc, gestimator.cc, getopt.c, getopt.h,
	  getopt1.c, getoptFix.h, polydNdSbase.cc, rsq.cc, sharedPoly.cc,
	  snntest.cc: Updated use of "getopt" so that programs work on
	  Apple's "Leopard" (OS X 10.5.x).  Testing suggests backwards
	  compatibility w/Tiger, too.

2007-11-29 09:38  kevin

	* aclocal.m4, configure, configure.in, mkinstalldirs: package 0.6.9

2007-11-29 09:38  kevin

	* src/: MKtestOutput.cc, Makefile.am, Makefile.in, chisq.c,
	  chisq.cc, chisq.h, chisq.hpp, compute_functions.cc, polydNdS.cc,
	  polydNdSbase.cc: updated code to be  C99 compliant: uses isfinite
	  instead of finite.  Changed the chisq files from C to C++ due to
	  odd linking problems that I could not figure out.  (I was having
	  trouble compiling them as C then linking them to the C++ program.
	  The linker could not find isfinite)

2006-06-22 07:08  kevin

	* ChangeLog, config.h.in, configure, configure.in: package 0.6.8

2006-06-22 05:04  kevin

	* src/: Makefile.am, Makefile.in, snn.cc, snntest.cc: renamed
	  snn.cc snntest.cc

2006-06-21 17:18  kevin

	* src/polydNdS.1: clarified documentation of -I option

2006-06-19 08:16  kevin

	* src/: descPoly.1, descPoly.cc, polyCommon.cc, polyCommon.hpp:
	  site frequency spectrum is now either folded or unfolded, rather
	  than based on minor allele frequency (which was a half-assed
	  thing to do in the first place).

2006-06-19 08:14  kevin

	* src/: compute_classes.cc, compute_functions.cc: now outputs
	  number of derived singletons for data sets with outgroup

2006-05-09 07:22  kevin

	* src/: Makefile.am, Makefile.in: fixed bug in snn_SOURCE

2006-05-09 07:17  kevin

	* configure, configure.in, debian/changelog, src/Makefile.am,
	  src/Makefile.in: package 0.6.8

2006-05-09 07:16  kevin

	* src/snn.cc: program to execute Hudson's Snn test

2006-05-04 11:58  kevin

	* src/compute_functions.cc: some changes to output to be more
	  R-friendly.

2006-05-04 11:45  kevin

	* src/compute_classes.cc: added a missing output of '\n' so that
	  output from compute is as it should be when -V and -p are used in
	  combination

2006-03-05 13:39  kevin

	* configure, configure.in, debian/changelog: package 0.6.7

2006-03-05 13:34  kevin

	* src/compute_classes.cc: now output nan for undefined values of
	  Rmin

2005-09-20 11:54  kevin

	* debian/changelog: package 0.6.6

2005-09-06 09:14  kevin

	* src/polydNdS.1: updated man page to correctly describe -I

2005-08-31 07:55  kevin

	* debian/changelog: corrected day entry for 0.6.6

2005-08-31 07:51  kevin

	* configure, configure.in, debian/changelog: pacakge 0.6.6

2005-08-31 07:43  kevin

	* src/compute_classes.cc: coalescent simulation now compatible with
	  libsequence 1.5.9

2005-08-31 07:42  kevin

	* src/compute_functions.cc: changed output to be more R-friendly

2005-08-31 07:42  kevin

	* src/compute.cc: when writing to a file, outfile stream is now
	  flushed to make sure that all output gets written

2005-06-07 04:17  kevin

	* src/chisq.c: now checks that chisq values are finite, and if not,
	  gives nan as a pvalue

2005-06-06 04:55  kevin

	* configure, configure.in, debian/changelog: package 0.6.5

2005-06-05 09:50  kevin

	* src/compute_classes.cc: definition of removeFixedInsertions is no
	  longer recurive.  The recursive implementation caused segfaults
	  on some systems when processing very large alignments

2005-05-27 13:05  kevin

	* configure, configure.in, debian/changelog: package 0.6.4

2005-05-27 12:59  kevin

	* src/: Makefile.am, Makefile.in: added requirement for gsl for
	  compute

2005-05-27 12:58  kevin

	* src/MKtest.1: clarified some of the documentation

2005-05-27 12:57  kevin

	* src/: compute_classes.cc, compute_classes.hpp,
	  compute_functions.cc: updated to coalescent simulation code in
	  libsequence 1.5.4

2005-04-29 12:40  kevin

	* aclocal.m4, config.h.in, configure, configure.in,
	  debian/changelog: package 0.6.3

2005-04-29 12:38  kevin

	* src/descPoly.cc: removed an extraneous ; that caused problems
	  with gcc 3.4

2004-11-03 14:19  kevin

	* configure, configure.in, debian/changelog: package 0.6.2

2004-11-03 14:18  kevin

	* src/rsq.cc: no longer outputs dij column

2004-11-03 14:18  kevin

	* src/compute_classes.cc: no longer exits with error if outgroup
	  number is > 1

2004-10-05 12:07  kevin

	* configure, configure.in, debian/changelog: package 0.6.1

2004-10-05 12:06  kevin

	* src/compute.1: documented defining outgroup more accurately

2004-10-05 12:06  kevin

	* src/CodonMaker.cc: added extra check to ensure codons chosen are
	  not identical

2004-10-05 12:05  kevin

	* src/: cRPimpl.cc, cRPimpl.hpp, polydNdS.cc, polydNdSbase.cc:
	  fixed several "special case" bugs in processing coding regions.
	  Thanks to Josh Shapiro for pointing these out & providing fixes

2004-10-05 12:04  kevin

	* src/: compute.cc, compute_classes.cc, compute_classes.hpp,
	  compute_functions.cc: better reporting of "not applicable" in
	  output when summary stats can't be calculated since there are too
	  few seg sites

2004-07-02 07:29  kevin

	* src/compute_functions.hpp: changed function declarations

2004-07-02 07:29  kevin

	* src/rsq.cc: now outputs both site positions and the distance b/w
	  sites

2004-07-02 07:26  kevin

	* src/rsq.1: updated to new behavior of the Disequilibrium()
	  routine in libsequence

2004-04-14 10:43  kevin

	* src/: Makefile.am, Makefile.in, compute.cc, compute_classes.cc,
	  compute_classes.hpp, compute_functions.cc, compute_functions.hpp:
	  compute is now object based rather than procedural

2004-04-12 15:12  kevin

	* configure, configure.in, debian/changelog: package 0.6.0

2004-04-12 15:12  kevin

	* src/compute_functions.cc: pvalue for fay-wu H now done correctly

2004-04-12 08:32  kevin

	* debian/changelog: updated to 0.5.9-1, compiled vs libsequence
	  1.3.9

2004-04-08 07:00  kevin

	* configure, configure.in, debian/changelog: package version 0.5.9

2004-04-08 06:57  kevin

	* src/compute_functions.cc: removed use of deprecated header
	  <Sequence/Hudson2001.hpp>

2004-04-08 06:53  kevin

	* src/MKtest.cc: added an extra check to the counting of fixed
	  differences that should prevent the possibility of (rare)
	  miscounts

2004-04-08 06:52  kevin

	* src/polyCommon.cc: removed use of deprecated libsequence typedefs

2004-04-08 06:51  kevin

	* src/: rsq.cc, sharedPoly.cc: removed inclusion of deprecated
	  libsequence headers

2004-02-02 09:36  kevin

	* configure, configure.in, debian/changelog, debian/control:
	  package 0.5.8

2004-02-02 09:25  kevin

	* src/: CodonMaker.cc, MKtest.cc, MKtestOutput.cc,
	  MKtestOutput.hpp, Makefile.am, Makefile.in, cRPimpl.cc,
	  cRPimpl.hpp, codingRegionProcessor.cc, codingRegionProcessor.hpp,
	  polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp, sharedPoly.cc:
	  calculation of silent and replacement poly now uses routines in
	  <Sequence/shortestPath.hpp>, allowing for a much cleaner
	  implementation of these programs

2004-01-20 12:22  kevin

	* configure, configure.in, debian/changelog: package 0.5.7 : bugfix
	  release.  SNP tables for MKtest now generated correctly

2004-01-20 12:12  kevin

	* src/MKtest.cc: There was a bug in generating the SNP tables for
	  each locus.  Josh Shapiro caught it, and its now fixed. They were
	  being generated from the data object, rather than gene1 and
	  gene2.

2004-01-19 06:04  kevin

	* configure, configure.in, debian/changelog, src/Makefile.am,
	  src/Makefile.in: package 0.5.6 : autoconf now checks for GSL
	  headers.  If they are present, -DHAVE_GSL is passed to the
	  compiler.  This is used in MKtest to decide if the G-test and
	  chi-squared tests will be compiled in, which only happens if
	  HAVE_GSL is defined

2004-01-19 05:58  kevin

	* src/: MKtest.cc, chisq.c, chisq.h, g2.c, g2.h: now checks for #if
	  defined (HAVE_GSL) to decide whether or not to calculate G-test
	  and chi-squared tests

2004-01-19 05:57  kevin

	* src/cRPimpl.cc: simplified checking for stop codons

2004-01-19 05:56  kevin

	* src/polyCommon.cc: uses Sequence::SEQMAXUNSIGNED now instead of
	  defining a new constant

2004-01-19 05:56  kevin

	* src/: compute.cc, compute_functions.cc, compute_functions.hpp:
	  uses new implementation of coalescent algorithm
	  (Sequence::coalNoRec)

2004-01-12 15:35  kevin

	* src/compute_functions.cc: now exits with error if input data
	  contain characters other than {A,G,C,T,N,-}

2004-01-12 08:08  kevin

	* aclocal.m4, configure, configure.in, debian/changelog,
	  debian/control: package 0.5.4

2004-01-12 07:18  kevin

	* src/: codingRegionProcessor.cc, codingRegionProcessor.hpp: new
	  files

2004-01-12 07:07  kevin

	* src/compute.1: update to document new options

2004-01-12 07:06  kevin

	* src/tstvbias.cc: cleanup

2004-01-12 07:06  kevin

	* src/: MKtest.cc, cRPimpl.cc, gestimator.cc, translateCoding.cc:
	  updated to new header <Sequence/Translate.hpp>

2004-01-11 12:39  kevin

	* src/compute_functions.cc: now removes sites with characters other
	  than {A,G,C,T}

2004-01-11 12:29  kevin

	* src/: compute.cc, compute_functions.cc, compute_functions.hpp:
	  added new option, -N, to remove all sites w/missing data.  Fixed
	  a bug in compute where the -b option had no effect if data were
	  input with the -h option

2003-11-11 07:49  kevin

	* configure, configure.in, debian/changelog, debian/control,
	  src/Makefile.am, src/Makefile.in: package 0.5.4

2003-11-11 07:31  kevin

	* src/: Fexact_main.cc, HBKpermute.cc, MKtest.cc, Makefile.am,
	  Makefile.in, compute.cc, compute_functions.cc, descPoly.cc,
	  distance.cc, extractCoding.cc, fexact.c, gestimator.cc,
	  int_handler.cc, polyCommon.cc, polydNdS.cc, polydNdSbase.cc,
	  polydNdSbase.hpp, rsq.cc, sharedPoly.cc, translateCoding.cc,
	  tstvbias.cc: Lots of changes: 1.) new classes for MKtest,
	  polydNdS to help streamline maintenance 2.) #include "foo.h"
	  changed to #include <foo.h> all over

2003-11-11 07:31  kevin

	* src/: CodonMaker.cc, CodonMaker.hpp, Warnings.cc, Warnings.hpp,
	  cRPimpl.cc, cRPimpl.hpp: new classes to simplify
	  silent/replacement poly calculations

2003-11-11 07:27  kevin

	* src/chisq.c: fixed bug that caused n to be calculated incorrectly

2003-10-28 12:19  kevin

	* src/: tajd.cc, tajd.1: removed

2003-10-28 12:18  kevin

	* src/gestimator.cc: cleanup

2003-10-27 11:25  kevin

	* src/gestimator.cc: now exits with an error if infile cannot be
	  opened

2003-10-27 07:32  kevin

	* src/MKtest.cc: cleanup

2003-10-27 07:29  kevin

	* src/: MKtest.cc, polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp:
	  process_coding_region() in polydNdSbase.cc now returns a
	  container (class Warnings) containing any warnings that arose
	  during processing of the data.  polydNdS.cc and MKtest.cc are
	  updated to print such data to stderr.

2003-10-27 07:15  kevin

	* src/: MKtest.cc, extractCoding.cc, translateCoding.cc: now catch
	  exceptions when calling parseargs

2003-10-27 07:15  kevin

	* src/polydNdSbase.cc: moved more error checking in parseargs from
	  cerr followed by exit(1) to an exception-based strategy

2003-10-26 09:23  kevin

	* src/compute_functions.cc: now checks that data file can be
	  read...

2003-10-26 09:22  kevin

	* src/polydNdS.cc: now makes sure that infile for alignment is
	  available for reading

2003-10-26 09:13  kevin

	* src/: compute.cc, compute_functions.cc, compute_functions.hpp,
	  polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp, rsq.cc: now do
	  stricter checking to make sure infiles exist

2003-10-15 07:56  kevin

	* src/gestimator.cc: now, all exceptions really are printed to
	  stderr :)!

2003-10-15 07:55  kevin

	* src/gestimator.cc: fixed typo

2003-10-15 07:54  kevin

	* src/gestimator.cc: output from all exception catching is now
	  output to stderr

2003-10-15 07:53  kevin

	* src/: Makefile.in, translateCoding.cc: for translateCoding, will
	  default to translating the entire alignment if no other input are
	  given

2003-09-10 11:25  kevin

	* src/: Correlations.hpp, Makefile.am, Makefile.in,
	  RandomNumbers.hpp, polydNdSbase.cc: added new files (to remove
	  dependency on my now-defunct cpptools package).  modified
	  polydNdSbase.cc to compile in the face of the g++ bug that causes
	  infinited compiler recursion for templates in anonymous
	  namespaces

2003-09-08 07:38  kevin

	* src/: extractCoding.cc, translateCoding.cc: added #include
	  <iostream>

2003-09-05 11:39  kevin

	* src/: MKtest.cc, compute_functions.cc, compute_functions.hpp,
	  polydNdSbase.cc, polydNdSbase.hpp: removed references to
	  namespace Comparisons (which no longer exists), code now
	  namespace-clean in general

2003-09-03 09:02  kevin

	* src/: HBKpermute.cc, MKtest.cc, chud.cc, compute_functions.cc,
	  compute_functions.hpp, descPoly.cc, distance.cc, dists.cc,
	  extractCoding.cc, gestimator.cc, polyCommon.cc, polyCommon.hpp,
	  polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp, rsq.cc,
	  sharedPoly.cc, translateCoding.cc, tstvbias.cc: updated to new
	  libsequence structure (#include<Sequence/foo.hpp>)

2003-08-13 09:50  kevin

	* debian/changelog: package version 0.5.2

2003-08-13 09:49  kevin

	* configure, configure.in: package 0.5.2

2003-08-13 09:47  kevin

	* src/: polydNdS.1, polydNdS.cc: added -A option and documented it
	  in manpage

2003-08-07 07:34  kevin

	* debian/changelog: package revision 0.5.1-2, compiled against
	  libsequence 1.3.2

2003-08-06 09:04  kevin

	* configure, configure.in, debian/changelog, debian/control:
	  package 0.5.1

2003-08-06 09:03  kevin

	* src/MKtest.1: added newline to fix formatting of manpage

2003-08-06 08:37  kevin

	* src/sharedPoly.cc: machinery for calculations now uses class
	  Sequence::FST from libsequence

2003-07-25 10:53  kevin

	* src/polydNdS.1: more changes

2003-07-25 10:50  kevin

	* src/polydNdS.1: updated manpage

2003-07-25 10:46  kevin

	* src/: MKtest.1, sharedPoly.1: updated manpages

2003-07-22 10:48  kevin

	* debian/changelog: package version 0.5.0 (not 0.5.9!)

2003-07-22 10:44  kevin

	* configure, configure.in, debian/changelog: package 0.5.0

2003-07-18 08:50  kevin

	* src/sharedPoly.cc: rewrote code to handle all sorts of special
	  cases, including 3 mutations/site.  These changes will eventually
	  be incorporated into the FST class in libsequence

2003-07-15 07:25  kevin

	* Makefile.in, aclocal.m4, configure, configure.in,
	  debian/changelog: package 0.4.9

2003-07-15 07:16  kevin

	* src/MKtest.cc: rewrote starting from a much simpler perspective.
	  now seems to work much better in general.

2003-07-15 07:16  kevin

	* src/: polydNdSbase.cc, polydNdSbase.hpp: near-complete rewrite.
	  much simpler (and shorter) code does the same thing as the old,
	  clunky version.

2003-07-11 07:08  kevin

	* src/: Makefile.am, Makefile.in: [no log message]

2003-07-11 07:06  kevin

	* src/: polydNdSbase.cc, polydNdSbase.hpp: added option to
	  process_coding_region() to allow approximate treatment of
	  ambiguous/completely substituted codons.  NOTE: not fully
	  implemented yet.

2003-07-11 07:05  kevin

	* src/MKtest.cc: a near-complete re-write of the internals.  added
	  options for approximate treatment of divergent codons when
	  calculating divergence.

2003-07-09 12:39  kevin

	* src/: polydNdSbase.cc, polydNdSbase.hpp: MakeCodon() no longer
	  needs a PolySites*, various cleanup

2003-07-07 09:55  kevin

	* src/translateCoding.cc: new file

2003-07-07 06:15  kevin

	* src/polydNdSbase.cc: now outputs what the stop codon is when a
	  stop codon is encountered

2003-07-01 05:49  kevin

	* src/: Makefile.am, Makefile.in: new program "Fexact"

2003-07-01 05:48  kevin

	* src/sharedPoly.cc: added -v option for verbose output

2003-07-01 05:48  kevin

	* src/polydNdSbase.hpp: added	bool XtractFullCodons; to arguments
	  struct

2003-07-01 05:47  kevin

	* src/polydNdSbase.cc: -X and -T options added to parseargs,
	  position of ambiguous pathways is now output

2003-07-01 05:47  kevin

	* src/polydNdS.cc: cleanup of output code

2003-07-01 05:46  kevin

	* src/extractCoding.cc: now deals with input of CDS intervals
	  better

2003-07-01 05:45  kevin

	* src/compute_functions.cc: floats changed to doubles

2003-07-01 05:45  kevin

	* src/MKtest.cc: program now accepts -T to output tab-delimited
	  table (not documented yet in man page)

2003-07-01 05:44  kevin

	* src/Fexact_main.cc: new file

2003-06-18 09:07  kevin

	* ChangeLog, configure, configure.in, debian/changelog: package
	  version 0.4.8

2003-06-18 09:04  kevin

	* src/: MKtest.1, compute.1, polydNdS.1: updated manpages

2003-06-18 08:54  kevin

	* src/: polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp: massive
	  bugfixes, diagnostic info now printed to stderr.

2003-06-18 08:54  kevin

	* src/: Makefile.am, Makefile.in: new source files:
	  translateCoding.cc and extractCoding.cc

2003-06-18 08:52  kevin

	* src/MKtest.cc: cleanup

2003-06-18 08:52  kevin

	* src/extractCoding.cc: new program

2003-06-18 08:51  kevin

	* src/compute_functions.cc: now, positions of SNPs are along the
	  alignment as it is input, rather than from the first ungapped
	  position

2003-06-07 13:25  kevin

	* src/polydNdS.1: updated documentation

2003-06-07 13:20  kevin

	* src/: Makefile.in, tstvbias.cc: cleanup

2003-06-07 12:45  kevin

	* src/: HBKpermute.cc, Makefile.am, compute.cc,
	  compute_functions.hpp, descPoly.cc, distance.cc, polyCommon.cc,
	  polyCommon.hpp, polydNdS.1, rsq.cc, sharedPoly.cc, tstvbias.cc:
	  fixed includes for non-GNU systems. portability to gcc 2.95. now
	  use portability header getoptFix.h

2003-06-07 12:44  kevin

	* src/getoptFix.h: portability header for getopt

2003-06-07 12:43  kevin

	* src/: compute_functions.cc, gestimator.cc: changed an unsigned to
	  an int to remove compiler warning

2003-06-07 12:43  kevin

	* src/: MKtest.cc, polydNdS.cc:  now optionally skips missing data
	  using -S option from polydNdSbase.cc

2003-06-07 12:42  kevin

	* src/polydNdSbase.hpp: added skipMissing to parameters struct

2003-06-07 12:42  kevin

	* src/polydNdSbase.cc:	-I option now works. Added -S option to
	  parseargs so that polydNdS and MKtest can optionally skip sites
	  w/missing data. Added #include<algorithm>

2003-06-05 06:26  kevin

	* ChangeLog, configure, configure.in, debian/changelog: package
	  version 0.4.7

2003-06-03 14:19  kevin

	* src/polydNdSbase.cc: fixed bug in InCoding(int site_index, const
	  vector<int> &intervals).  The bug was that the value 1 was
	  subtracted from each interval position.  This was incorrect
	  because the intervals are already indexes.

2003-06-03 11:58  kevin

	* ChangeLog, configure, configure.in, debian/changelog,
	  src/Makefile.in: package version 0.4.6

2003-06-03 11:58  kevin

	* src/Makefile.am: added manpages to source lists

2003-06-03 11:56  kevin

	* src/: descPoly.1, descPoly.cc, sharedPoly.1: added man pages

2003-06-03 11:46  kevin

	* src/: descPoly.cc, polyCommon.cc, polyCommon.hpp: new program
	  added (descPoly)

2003-06-03 08:51  kevin

	* src/polydNdSbase.cc: Fixed bug in DetermineOnePoly(const
	  PolyTable *poly_table, int codon_pos,int i) that mistakenly
	  returned false for cases where there is only 1 SNP in the entire
	  data set.

2003-06-02 12:15  kevin

	* src/polydNdS.cc: the previous "fix" for mis-assigned coding SNPs
	  was incorrect.  This has now been fixed by using the InCoding()
	  routine

2003-06-02 10:26  kevin

	* src/: Makefile.am, Makefile.in, compute_functions.cc,
	  polydNdS.cc, polydNdSbase.cc: cleanup

2003-06-02 08:20  kevin

	* src/polydNdS.cc: fixed bug where sites that were skipped for some
	  reason in the coding region could be mistakenly considered to be
	  noncoding

2003-05-23 12:43  kevin

	* src/sharedPoly.cc: added try/catch block

2003-05-23 12:32  kevin

	* src/: Makefile.am, Makefile.in, sharedPoly.cc: added program
	  "sharedPoly"

2003-05-19 09:32  kevin

	* configure, configure.in, debian/changelog: package 0.4.5

2003-05-16 15:04  kevin

	* src/compute_functions.cc: updated code comments

2003-05-16 15:02  kevin

	* src/compute_functions.cc: now, if there is no polymorphism in the
	  data, the following statistics are output as NA: Tajima's D,
	  Fu/Li statistics, Wall's statistics, Rmin, and Hudson's C

2003-05-16 14:30  kevin

	* src/: Makefile.am, Makefile.in: removed tajd.1 from man_MANS so
	  that deb package can be built

2003-05-16 14:14  kevin

	* configure, configure.in, debian/changelog: package 0.4.4

2003-05-16 14:02  kevin

	* src/compute_functions.cc: now handles data with no seg sites
	  properly with -p option (outputs NA for each statistic)

2003-05-07 08:32  kevin

	* src/g2.c: removed "adding 1 to everything" in the case of zero
	  counts.  Just doesn't seem right to me...

2003-05-07 08:31  kevin

	* src/: Makefile.am, Makefile.in: removed silly programs (that are
	  now replaced by msld and msstats packages anyways).  added
	  manpage for MKtest

2003-05-07 08:30  kevin

	* src/g2.c: removed all numerical recipes code.

2003-05-07 08:28  kevin

	* src/MKtest.cc: halved number of loops over data structures.  now
	  output chisquare and G-tests where possible

2003-05-07 08:27  kevin

	* src/MKtest.1: added manpage

2003-05-07 08:26  kevin

	* src/: chisq.c, chisq.h: added Yate's correction.  Simplified
	  formula for calculation.

2003-05-06 11:50  kevin

	* src/polydNdS.cc: code cleanup

2003-05-05 08:26  kevin

	* configure, configure.in, debian/changelog: package 0.4.3

2003-05-05 08:24  kevin

	* src/: Makefile.am, Makefile.in: MKtest removed from list of
	  programs to compile (not ready yet...)

2003-05-05 08:12  kevin

	* src/: polydNdSbase.cc, polydNdSbase.hpp: fixed bug where codon
	  position of a mutation was incorrectly calculated. The bug was in
	  GetCodonPos()

2003-05-05 08:11  kevin

	* src/polydNdS.cc: Pi is now output per site

2003-05-05 08:11  kevin

	* src/g2.c: replaced computation of p-value by Num. Rec. code with
	  GSL routines

2003-05-05 08:08  kevin

	* src/chisq.c: [no log message]

2003-05-05 08:08  kevin

	* src/MKtest.cc: removed predicate functions (they didn't work :(
	  ), now do calculations with explicit loops. Modified output
	  format.

2003-05-03 13:49  kevin

	* src/: polydNdSbase.cc, polydNdSbase.hpp: fixed 2 bugs.  The first
	  resulted in mis-assigning the position in a codon of mutations at
	  positions 1 or 2 (position 3 was fine).  the second was a pass by
	  value of a vector instead of by reference.

2003-05-03 08:42  kevin

	* src/: ctest.h, fexact.c: added source files for Fisher's exact
	  test, from the R project (http://www.r-project.org)

2003-05-03 08:41  kevin

	* src/: HBKpermute.cc, MKtest.cc, Makefile.am, Makefile.in,
	  chisq.c, chisq.h, chud.cc, compute.cc, compute_functions.cc,
	  compute_functions.hpp, distance.cc, dists.cc, g2.c, g2.h,
	  gestimator.cc, polydNdS.cc, polydNdSbase.cc, polydNdSbase.hpp,
	  rsq.cc, tajd.cc, tstvbias.cc, tstvbias.hpp: reformatted files
	  with astyle. Added code for MK tests, which required pulling code
	  from polydNdS and putting it in polydNdSbase so the 2 programs
	  could share

2003-04-04 09:36  kevin

	* src/gestimator.cc: removed out old (commented-out) code

2003-04-04 09:35  kevin

	* src/gestimator.cc: only #include "Fasta.hpp" on non-GNU compilers

2003-04-04 08:55  kevin

	* debian/changelog: updated package version #

2003-04-04 08:54  kevin

	* configure, configure.in: package 0.4.2

2003-04-04 08:53  kevin

	* src/rsq.cc: changed an #include directive to allow compilation on
	  systems without BOOST installed

2003-04-03 14:12  kevin

	* src/: HBKpermute.cc, compute_functions.cc, distance.cc,
	  gestimator.cc, polydNdS.cc, rsq.cc: upgraded to take advantage of
	  explicit instantiations in libsequence

2003-04-03 08:52  kevin

	* debian/changelog: updated package version #

2003-04-03 08:52  kevin

	* configure: [no log message]

2003-04-03 08:37  kevin

	* configure.in: updated package version to 0.4.1

2003-04-03 08:37  kevin

	* src/polydNdS.cc: updated to new version of
	  Sequence::Aligment::Trim( const vector<T>& , const vector<int> &)

2003-04-02 08:45  kevin

	* src/compute_functions.cc: added Wall's statistics to output

2003-04-02 08:45  kevin

	* Makefile.in: [no log message]

2003-04-01 09:23  kevin

	* Makefile.am, debian/README.debian, debian/analysis-doc.files,
	  debian/changelog, debian/control, debian/copyright,
	  debian/crontab.ex, debian/dirs, debian/diversions.ex,
	  debian/files, debian/inetd.conf.ex, debian/info.ex,
	  debian/init.d.ex, debian/manpage.1.ex, debian/menu.ex,
	  debian/rules, debian/substvars, debian/watch.ex: added debian
	  build dir

2003-03-24 08:05  kevin

	* src/: HBKpermute.cc, chud.cc, compute_functions.hpp, distance.cc,
	  dists.cc, gestimator.cc, polydNdS.cc, tajd.cc: added "using
	  namespace Sequence"

2003-03-21 09:29  kevin

	* configure, configure.in: package 0.4.0

2003-03-21 09:28  kevin

	* src/: tstvbias.cc, tstvbias.hpp: updated to use
	  Sequence::stateCounter class

2003-03-21 09:28  kevin

	* src/polydNdS.1: updated man page

2003-03-21 09:27  kevin

	* src/polydNdS.cc: made reading in of file cleaner

2003-03-21 09:27  kevin

	* src/: Makefile.am, Makefile.in: added HBKpermute

2003-03-21 09:27  kevin

	* src/: HBKpermute.1, HBKpermute.cc: added program to package

2003-03-15 10:11  kevin

	* src/compute_functions.cc: fixed error in output (forgot a tab in
	  outputting # Singletons)

2003-03-14 12:52  kevin

	* src/: HBKpermute.cc, chud.cc, dists.cc, gestimator.cc,
	  polydNdS.cc, tajd.cc: update to PolySNP and PolySIM classes

2003-03-14 10:48  kevin

	* src/rsq.cc: updated from Poly to PolySNP

2003-03-13 15:09  kevin

	* src/: compute_functions.cc, compute_functions.hpp: upgraded to
	  new PolySNP and PolySIM classes

2003-02-26 14:22  kevin

	* src/rsq.cc: made friendlier if no infile specified

2003-02-26 14:20  kevin

	* src/polydNdS.cc: updated to new range operation version of
	  Sequence::Translate()

2003-02-21 11:04  kevin

	* src/: compute_functions.cc, rsq.cc: package version 1.1.9--no
	  longer convert to binary data when analyzing Rm or linkage
	  disequilibrium

2003-02-21 11:03  kevin

	* configure: package version 1.1.9

2003-02-21 11:02  kevin

	* configure.in: package version 0.3.9

2003-02-17 12:13  kevin

	* src/compute_functions.cc: cleanup

2003-02-17 12:11  kevin

	* src/compute_functions.cc: fixed bug in read() where I allocated 1
	  to many characters to the outgroup string, resulting in bad
	  behavior

2003-01-20 08:19  kevin

	* configure, configure.in: package 0.3.8 -- works with g++ 3.1 on
	  OS X

2003-01-18 12:46  kevin

	* src/: chud.cc, compute.cc, distance.cc, dists.cc, gestimator.cc,
	  polydNdS.cc, rsq.cc, tajd.cc: no longer includes getopt.h on OS X
	  systems

2003-01-18 10:14  kevin

	* ChangeLog: updated ChangeLog :)

2003-01-18 10:14  kevin

	* src/compute_functions.cc: added some missing #include

2003-01-14 13:48  kevin

	* src/dists.cc: fixed typos...

2003-01-14 13:47  kevin

	* src/rsq.cc: updated to new version of Numerology::ProductMoment

2003-01-14 09:55  kevin

	* src/rsq.cc: added a typedef

2003-01-13 13:26  kevin

	* src/tajd.cc: added more info to output:expectsion, critical
	  values, etc.

2003-01-13 12:22  kevin

	* configure, configure.in: package version 0.3.6

2003-01-13 12:21  kevin

	* src/: Makefile.am, Makefile.in, crit.c, crit.h, dists.cc, rsq.cc,
	  tajd.cc: updated to new routines in my cpptools package--results
	  in faster code!

2003-01-10 11:14  kevin

	* src/dists.cc: removed unecessary cout of sorted vector

2003-01-10 11:14  kevin

	* src/dists.cc: removed some unecessary variables

2003-01-04 17:41  kevin

	* src/: Makefile.am, Makefile.in, compute_functions.cc, crit.c,
	  num_comparisons.c, num_comparisons.h: removed num_comparisons.*

2003-01-02 18:45  kevin

	* src/gestimator.cc: removed out of data comments

2002-11-25 09:59  kevin

	* configure.in: package version 1.0.8

2002-11-25 09:55  kevin

	* src/rsq.cc: added D' back to output, -c option now works

2002-11-24 10:36  kevin

	* src/: Makefile.am, Makefile.in, chud.cc, rsq.cc: removed
	  HBKPermute program, removed D' from rsq

2002-11-24 10:36  kevin

	* configure, configure.in: package version 0.3.3

2002-10-26 10:32  kevin

	* src/: HBKpermute.cc, Makefile.am, Makefile.in, Permutations.cc,
	  Permutations.hpp: made changes to HBKPermute: fixed bug in
	  calculation of Fst (I think), and moved contents of
	  Permutations.* to HBKPermute.cc

2002-10-26 10:31  kevin

	* configure, configure.in: updated package version to 0.3.2

2002-10-22 13:29  kevin

	* src/polydNdS.cc: various cleanups

2002-09-20 11:34  kevin

	* src/tajd.cc: cleanup

2002-09-20 11:33  kevin

	* Makefile.in, aclocal.m4: [no log message]

2002-09-19 18:06  kevin

	* Makefile.in, aclocal.m4, configure, configure.in,
	  src/Makefile.am, src/Makefile.in, src/dists.cc, src/tajd.cc:
	  removed dependency on gsl

2002-09-13 09:26  kevin

	* src/: Makefile.am, Makefile.in: removed HBKPermute as a target
	  until I fix the bugs

2002-09-05 11:40  kevin

	* src/: compute.1, polydNdS.1: documented new CLI options

2002-09-05 11:35  kevin

	* src/compute_functions.cc: added checks for 0 in output routine

2002-09-05 11:32  kevin

	* src/compute_functions.cc: -P now works with -h

2002-09-05 11:32  kevin

	* src/compute.cc: when using -P, -s is now implied

2002-09-05 11:28  kevin

	* src/compute_functions.hpp: removed output2 prototype

2002-09-05 11:28  kevin

	* src/compute_functions.cc: removed hack for Hudson2001 format--it
	  all works as it should now

2002-09-05 10:10  kevin

	* src/compute_functions.cc: added a hack so that hudson2001 format
	  is supported.  Will not count Rmin :(.

2002-09-05 09:25  kevin

	* src/polydNdS.cc: cleanup up language in output to prevent
	  ambiguity. also fixed some bugs regarding conssistency of index
	  vs. position (a consistenly annoying problem with this program).

2002-09-04 10:02  kevin

	* src/: compute.cc, compute_functions.hpp: added option to use poly
	  table as input

2002-09-04 09:59  kevin

	* src/polydNdS.cc: fixed typo in comment

2002-09-04 09:32  kevin

	* src/polydNdS.cc: added analysis and output of table for silent
	  +intron/flanking positions

2002-09-04 08:45  kevin

	* src/polydNdS.cc: made modifications so that positions of all
	  polymorphism tables are correct.  To date, the positions of
	  intron+flanking is not correct

2002-09-03 14:50  kevin

	* src/polydNdS.cc: added analysis of all silent ( = synonymous +
	  intron/flanking ) polymorphisms

2002-08-15 09:14  kevin

	* src/: Makefile.in, compute.cc, compute_functions.cc: fixed
	  portability problems to Sun systems

2002-08-14 11:38  kevin

	* src/Makefile.am: fixed source lists so that make dist works

2002-08-13 09:25  kevin

	* src/rsq.cc: update to new "generic algorithm" interface for
	  permutation tests

2002-08-12 11:05  kevin

	* src/rsq.cc: now use auto_ptr for Hudson2001 object for exception
	  safety (although prog exits if exceptions are caught, its nice to
	  be clean).

2002-08-12 09:55  kevin

	* src/Permutations.cc: added using namespace std; for g++-3.1's
	  benefit..

2002-08-12 09:52  kevin

	* src/int_handler.cc: added std::foo to make g++-3.1 happy

2002-08-12 07:25  kevin

	* src/: HBKpermute.cc, compute_functions.cc, compute_functions.hpp,
	  distance.cc, gestimator.cc, polydNdS.cc, rsq.cc: update to
	  changes in libsequence re: vectors

2002-08-06 09:45  kevin

	* src/: Makefile.am, Makefile.in, rsq.1, rsq.cc: updated to use
	  namespace Numerology

2002-08-05 08:25  kevin

	* src/rsq.cc: changed signficance testing code to use array
	  versions of templates instead of vectors

2002-08-01 12:53  kevin

	* src/: rsq.1, rsq.cc: update to allow frequency filters

2002-08-01 09:28  kevin

	* aclocal.m4, configure, configure.in, src/Makefile.am,
	  src/Makefile.in, src/compute_functions.cc: added --enable-debug
	  argument to configure

2002-07-29 13:34  kevin

	* src/: Makefile.am, Makefile.in, polyslide.cc: removed
	  polyslide.cc

2002-07-25 11:37  kevin

	* src/: HBKpermute.cc, Permutations.cc, Permutations.h,
	  Permutations.hpp, chud.cc, compute.cc, compute_functions.cc,
	  compute_functions.h, compute_functions.hpp, distance.cc,
	  dists.cc, gestimator.cc, int_handler.cc, int_handler.h,
	  int_handler.hpp, polydNdS.cc, polyslide.cc, rsq.cc, tajd.cc,
	  tstvbias.cc, tstvbias.h, tstvbias.hpp: .h to .hpp

2002-07-24 11:09  kevin

	* src/: polydNdS.cc, polyslide.cc: update to name change of
	  PolyData to PolyTable

2002-07-24 07:02  kevin

	* src/compute_functions.cc: fixed bug in estimating p-value for the
	  Depaulis-Veuille H statistic

2002-07-21 11:48  kevin

	* src/: chud.cc, compute_functions.cc, dists.cc, tajd.cc: added
	  using namespace std  where needed

2002-07-18 06:15  kevin

	* src/gestimator.cc: update to new libsequence conventions

2002-07-17 07:15  kevin

	* src/gestimator.cc: removed useless include of Translate.h

2002-07-17 07:15  kevin

	* src/polydNdS.cc: update to new Translate() machinery

2002-07-15 09:30  kevin

	* src/: num_comparisons.c, num_comparisons.h: added comments,
	  removed #include dependency on GNU scientific library

2002-07-15 09:29  kevin

	* src/compute_functions.cc: got rid of "one true brace" formatting

2002-07-15 09:21  kevin

	* src/compute_functions.cc: removed comment about a bug that has
	  been fixed

2002-07-15 09:20  kevin

	* src/: Makefile.am, Makefile.in, compute_functions.cc,
	  compute_functions.h: added new file

2002-07-15 09:20  kevin

	* src/compute.cc: moved functionality to compute_functions.h/.cc

2002-07-09 07:47  kevin

	* src/Makefile.am: fixed portability problem

2002-07-08 06:17  kevin

	* src/: Makefile.am, Makefile.in, SimDataSimple.cc,
	  SimDataSimple.h, compute.cc, ms_interface.cc, ms_interface.h,
	  ms_structs.h, msfunc.c, msfunc.h, rand1.c, rand1.h, streec.c,
	  streec.h: moved simulation engine to libsequence, modified
	  Makefiles and compute.cc to reflect the move

2002-07-04 16:16  kevin

	* src/compute.cc: modified checking of dvh to use fabs()

2002-07-04 16:12  kevin

	* src/: Makefile.am, Makefile.in, compute.cc, ms_interface.cc,
	  num_comparisons.c, rand1.c, crit.c: changed FLT_EPSILON to
	  DBL_EPSILON

2002-07-04 16:12  kevin

	* Makefile.in: [no log message]

2002-06-24 13:58  kevin

	* AUTHORS, COPYING, ChangeLog, INSTALL, Makefile.am, Makefile.in,
	  NEWS, README, acinclude.m4, aclocal.m4, analysis.lsm.in,
	  analysis.spec.in, config.guess, config.h.in, config.sub,
	  configure, configure.in, install-sh, missing, mkinstalldirs,
	  stamp-h.in, texinfo.tex, src/HBKpermute.1, src/HBKpermute.cc,
	  src/Makefile.am, src/Makefile.in, src/Permutations.cc,
	  src/Permutations.h, src/SimDataSimple.cc, src/SimDataSimple.h,
	  src/analysis.1, src/chud.cc, src/compute.1, src/compute.cc,
	  src/crit.c, src/crit.h, src/distance.cc, src/dists.cc,
	  src/gestimator.1, src/gestimator.cc, src/getopt.c, src/getopt.h,
	  src/getopt1.c, src/int_handler.cc, src/int_handler.h,
	  src/kimura80.1, src/ms_interface.cc, src/ms_interface.h,
	  src/ms_structs.h, src/msfunc.c, src/msfunc.h,
	  src/num_comparisons.c, src/num_comparisons.h, src/polydNdS.1,
	  src/polydNdS.cc, src/polyslide.cc, src/rand1.c, src/rand1.h,
	  src/rsq.1, src/rsq.cc, src/streec.c, src/streec.h, src/tajd.1,
	  src/tajd.cc, src/texinfo.tex, src/tstvbias.cc, src/tstvbias.h:
	  Initial revision

2002-06-24 13:58  kevin

	* AUTHORS, COPYING, ChangeLog, INSTALL, Makefile.am, Makefile.in,
	  NEWS, README, acinclude.m4, aclocal.m4, analysis.lsm.in,
	  analysis.spec.in, config.guess, config.h.in, config.sub,
	  configure, configure.in, install-sh, missing, mkinstalldirs,
	  stamp-h.in, texinfo.tex, src/HBKpermute.1, src/HBKpermute.cc,
	  src/Makefile.am, src/Makefile.in, src/Permutations.cc,
	  src/Permutations.h, src/SimDataSimple.cc, src/SimDataSimple.h,
	  src/analysis.1, src/chud.cc, src/compute.1, src/compute.cc,
	  src/crit.c, src/crit.h, src/distance.cc, src/dists.cc,
	  src/gestimator.1, src/gestimator.cc, src/getopt.c, src/getopt.h,
	  src/getopt1.c, src/int_handler.cc, src/int_handler.h,
	  src/kimura80.1, src/ms_interface.cc, src/ms_interface.h,
	  src/ms_structs.h, src/msfunc.c, src/msfunc.h,
	  src/num_comparisons.c, src/num_comparisons.h, src/polydNdS.1,
	  src/polydNdS.cc, src/polyslide.cc, src/rand1.c, src/rand1.h,
	  src/rsq.1, src/rsq.cc, src/streec.c, src/streec.h, src/tajd.1,
	  src/tajd.cc, src/texinfo.tex, src/tstvbias.cc, src/tstvbias.h:
	  initial commit of version 0.2.9