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ChangeLog
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ChangeLog
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------------------------------------------------------------------------
r1190 | kevin | 2009-01-23 16:37:32 -0800 (Fri, 23 Jan 2009) | 2 lines
package 1.6.5
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r1189 | kevin | 2009-01-23 16:31:09 -0800 (Fri, 23 Jan 2009) | 3 lines
Many changes with respect to typecasting and avoiding compiler
warnings. May break backwards-compatibility!
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r1188 | kevin | 2009-01-23 16:25:33 -0800 (Fri, 23 Jan 2009) | 2 lines
6-fold speed improvement to implementation of operator>>
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r1186 | kevin | 2007-11-29 09:34:43 -0800 (Thu, 29 Nov 2007) | 2 lines
package 1.6.5
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r1185 | kevin | 2007-11-29 09:34:24 -0800 (Thu, 29 Nov 2007) | 2 lines
Updated to use the C99 isfinite instead of the BSD finite
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r1183 | kevin | 2007-06-19 11:54:49 -0700 (Tue, 19 Jun 2007) | 2 lines
package 1.6.4
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r1182 | kevin | 2007-06-19 11:54:23 -0700 (Tue, 19 Jun 2007) | 2 lines
can now handle input woth- or without a label for the ancestral states. (this should be tested more!)
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r1181 | kevin | 2007-06-19 11:53:16 -0700 (Tue, 19 Jun 2007) | 2 lines
made changes so that haplotype counts are case-insensitive
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r1180 | kevin | 2007-06-19 11:52:26 -0700 (Tue, 19 Jun 2007) | 2 lines
cleanup
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r1179 | kevin | 2007-06-05 15:13:50 -0700 (Tue, 05 Jun 2007) | 2 lines
cleanup
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r1178 | kevin | 2007-06-05 15:13:28 -0700 (Tue, 05 Jun 2007) | 2 lines
cleanup
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r1177 | kevin | 2007-06-05 15:13:09 -0700 (Tue, 05 Jun 2007) | 2 lines
removed case-sensitivity
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r1176 | kevin | 2007-06-05 14:49:30 -0700 (Tue, 05 Jun 2007) | 2 lines
documented case-insensitivity of Different
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r1175 | kevin | 2007-06-05 14:37:07 -0700 (Tue, 05 Jun 2007) | 2 lines
made assignment using const_site_iterator types more efficient
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r1174 | kevin | 2007-06-05 14:36:03 -0700 (Tue, 05 Jun 2007) | 2 lines
added new constructor
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r1173 | kevin | 2007-06-05 14:31:20 -0700 (Tue, 05 Jun 2007) | 2 lines
cleanup
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r1172 | kevin | 2007-06-05 14:30:50 -0700 (Tue, 05 Jun 2007) | 2 lines
modified documentation
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r1171 | kevin | 2007-06-05 13:08:46 -0700 (Tue, 05 Jun 2007) | 2 lines
functions return immediately if table is empty
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r1170 | kevin | 2007-06-05 12:58:07 -0700 (Tue, 05 Jun 2007) | 2 lines
fixed bug in Different() where comparisons were not case-insensitive.
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r1169 | kevin | 2007-05-30 14:40:14 -0700 (Wed, 30 May 2007) | 2 lines
documented SimpleSNP::have_outgroup
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r1168 | kevin | 2007-05-30 14:39:18 -0700 (Wed, 30 May 2007) | 2 lines
added member function set_outgroup
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r1167 | kevin | 2006-09-06 17:14:17 -0700 (Wed, 06 Sep 2006) | 2 lines
functions now take non-const reference to a vector to store the path. function for selected alleles now works for non-const function objects
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r1166 | kevin | 2006-08-08 17:40:55 -0700 (Tue, 08 Aug 2006) | 2 lines
added figures. hopefully not corrupted..
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r1165 | kevin | 2006-08-08 17:40:15 -0700 (Tue, 08 Aug 2006) | 2 lines
removed
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r1163 | kevin | 2006-06-22 06:06:44 -0700 (Thu, 22 Jun 2006) | 2 lines
package 1.6.3
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r1162 | kevin | 2006-06-22 06:01:35 -0700 (Thu, 22 Jun 2006) | 2 lines
"make clean" now cleans up all the binaries
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r1161 | kevin | 2006-06-22 05:41:14 -0700 (Thu, 22 Jun 2006) | 2 lines
added documentation to one of the overloads of exponential_change
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r1160 | kevin | 2006-06-22 05:40:15 -0700 (Thu, 22 Jun 2006) | 2 lines
Added #include<Sequence/Coalescent/Trajectories.hpp>
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r1159 | kevin | 2006-06-22 05:33:09 -0700 (Thu, 22 Jun 2006) | 2 lines
header, and implementation file, for Coop & Griffiths-style simulation of trajectories of beneficial alleles. "Haploid" version implemented so far, version for general WF model is being worked on...
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r1158 | kevin | 2006-06-21 17:35:26 -0700 (Wed, 21 Jun 2006) | 2 lines
fixed bug in call to boost::bind
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r1157 | kevin | 2006-06-08 06:38:49 -0700 (Thu, 08 Jun 2006) | 2 lines
changed PermuteCorrelation to same interface model as coalescent simulations, with regards to random number objects.
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r1156 | kevin | 2006-05-05 12:10:03 -0700 (Fri, 05 May 2006) | 2 lines
new source files added
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r1155 | kevin | 2006-05-05 12:09:31 -0700 (Fri, 05 May 2006) | 2 lines
reverted back to more complex RNG-compatibility scheme, after reading about why std::random_shuffle works the way it does in Josuttis
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r1154 | kevin | 2006-05-05 10:31:43 -0700 (Fri, 05 May 2006) | 2 lines
removed forward delcarations to classes which don't exist
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r1153 | kevin | 2006-05-05 10:31:02 -0700 (Fri, 05 May 2006) | 2 lines
implementation classes now handled by std::auto_ptr
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r1152 | kevin | 2006-05-04 09:03:50 -0700 (Thu, 04 May 2006) | 2 lines
changed file documentation so that LaTeX manual now compiles without error
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r1151 | kevin | 2006-05-04 08:54:16 -0700 (Thu, 04 May 2006) | 2 lines
documented pick2_in_deme
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r1150 | kevin | 2006-05-04 06:59:31 -0700 (Thu, 04 May 2006) | 2 lines
reorganized make order so that valid_dna is linked last. this lest everything else finish up, in case an error occurs to to a lack of libboost_regex, which valid_dna requires
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r1149 | kevin | 2006-05-04 06:58:33 -0700 (Thu, 04 May 2006) | 2 lines
now demonstrates combination of boost::bind and gsl for random-number generation in coalescent simulation
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r1148 | kevin | 2006-05-04 06:57:41 -0700 (Thu, 04 May 2006) | 2 lines
updated to accomodate all the new files added to the project...
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r1147 | kevin | 2006-05-04 06:56:46 -0700 (Thu, 04 May 2006) | 2 lines
found a simpler way to make random-number generator compatibility nice and generric. functions now take objects, rather than references to the objects
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r1146 | kevin | 2006-05-04 06:55:09 -0700 (Thu, 04 May 2006) | 2 lines
changed function declarations so that they no longer take references to random-number generators. updated implementations to use Sequence/Portability/random_shuffle.hpp
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r1145 | kevin | 2006-05-04 06:53:32 -0700 (Thu, 04 May 2006) | 2 lines
definition of function Snn_statistic now matches prototype in Sequence/Snn.hpp
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r1144 | kevin | 2006-05-04 06:52:53 -0700 (Thu, 04 May 2006) | 2 lines
moved random_shuffl_wrapper.hpp to random_shuffle.hpp
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r1143 | kevin | 2006-05-04 05:26:39 -0700 (Thu, 04 May 2006) | 2 lines
changed to be a replacement for std::random_shuffle, since it's @%%@#%! broken
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r1142 | kevin | 2006-05-03 11:41:40 -0700 (Wed, 03 May 2006) | 2 lines
Hudson's Snn statistic and permutation test
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r1141 | kevin | 2006-05-03 11:33:52 -0700 (Wed, 03 May 2006) | 2 lines
added a check to assign(const_site_iterator beg,const_site iterator end) such that if (end-beg) < 1, the object will be empty and true will be returned
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r1140 | kevin | 2006-05-03 11:30:27 -0700 (Wed, 03 May 2006) | 2 lines
added these functions so that boost::bind can be used and still be compatible w/random_shuffle-like operations
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r1139 | kevin | 2006-05-03 11:04:42 -0700 (Wed, 03 May 2006) | 2 lines
added #include <Sequence/Coalescent/FragmentsRescaling.hpp>
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r1138 | kevin | 2006-05-03 11:03:56 -0700 (Wed, 03 May 2006) | 2 lines
added class newick_stream_marginal_tree. only output is supported right now, not input!
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r1137 | kevin | 2006-05-03 11:02:39 -0700 (Wed, 03 May 2006) | 2 lines
template functions now compatible with boost::bind + gsl random number interface combinations.
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r1136 | kevin | 2006-05-03 11:02:03 -0700 (Wed, 03 May 2006) | 2 lines
template functions more general with respect to random number generator compatibility. specifically, now compatible with boost::bind + gsl combos.
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r1135 | kevin | 2006-05-03 11:00:45 -0700 (Wed, 03 May 2006) | 2 lines
made template functions more general w/respect to random number generators. are now compatible w/boost::bind + gsl combos!
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r1134 | kevin | 2006-05-03 10:59:55 -0700 (Wed, 03 May 2006) | 2 lines
made template functions more general, and are now compatible with boost::bind + gsl random number generator combos
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r1133 | kevin | 2006-05-03 10:58:46 -0700 (Wed, 03 May 2006) | 2 lines
added interface for simulating partially-linked fragments
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r1132 | kevin | 2006-04-17 11:48:06 -0700 (Mon, 17 Apr 2006) | 2 lines
This function incorrectly returned nan if S=0. It now correctly returns 0.
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r1131 | kevin | 2006-04-17 11:47:49 -0700 (Mon, 17 Apr 2006) | 2 lines
added a quicker check for no variability to ThetaL()
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r1130 | kevin | 2006-03-28 06:38:01 -0800 (Tue, 28 Mar 2006) | 5 lines
changed implementation of minimize_arg in three ways:
1.) it now goes root to tips, instead of the other way around. this should be faster because trees that differ are more likely to differ at more ancient nodes
2.) For each node, the comparison of time is now done before the comparison of the ancestors
3.) The comparison of time in step 2 is now done using std::numeric_limits to account for the possibility of floating-point issues
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r1129 | kevin | 2006-03-26 07:22:28 -0800 (Sun, 26 Mar 2006) | 2 lines
fixed the exponential_change function to correctly handle the case of no growth
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r1128 | kevin | 2006-03-21 06:22:22 -0800 (Tue, 21 Mar 2006) | 2 lines
added template function pick2_in_deme
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r1126 | kevin | 2006-03-05 13:27:48 -0800 (Sun, 05 Mar 2006) | 2 lines
package 1.6.2
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r1125 | kevin | 2006-02-16 07:43:15 -0800 (Thu, 16 Feb 2006) | 2 lines
fixed bug in Disequilibrium(). When an outgroup was present, site i (in the pair i,j) kept having a base removed at each iteration, leading to incorrect values
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r1124 | kevin | 2006-01-26 06:34:16 -0800 (Thu, 26 Jan 2006) | 2 lines
fixed rare segfault in calculations of sliding windows. A test for a pointer being out of range was not done, causing the crashes.
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r1123 | kevin | 2006-01-13 07:59:05 -0800 (Fri, 13 Jan 2006) | 2 lines
when checking that population weights sum to 1, the check is now fab(sum-1.) > numeric_limits<double>::epsilon() to account for numeric precision
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r1121 | kevin | 2006-01-06 08:07:38 -0800 (Fri, 06 Jan 2006) | 2 lines
package 1.6.1
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r1120 | kevin | 2005-12-23 11:52:47 -0800 (Fri, 23 Dec 2005) | 2 lines
in function total_time_on_arg, there was a bug leading to an exception always being thrown. This was due to an inequality being tested as < , when > was what was intended. now fixed
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r1119 | kevin | 2005-12-20 17:02:56 -0800 (Tue, 20 Dec 2005) | 2 lines
In the calculation of D', the 11 gamete was ancestral/ancestral, rather than derived/derived. This is now fixed to match the documentation.
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r1118 | kevin | 2005-12-20 17:01:47 -0800 (Tue, 20 Dec 2005) | 2 lines
Fixed glitch in calculation of ThetaW. When totMuts==false, only the number of bi-allelic SNPs was used in the numerator of ThetaW. Now, the total number of variable sites is used, as intended.
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r1117 | kevin | 2005-12-09 09:48:03 -0800 (Fri, 09 Dec 2005) | 2 lines
added functions to calculate ThetaL and Hprime
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r1116 | kevin | 2005-12-09 06:41:00 -0800 (Fri, 09 Dec 2005) | 2 lines
Fixed minor error in calculation of f_hat which was pointed out by Andy Kern. I was taking the mean(f_hat) across loci as the estimate, rather than following equation 5 of the HKA paper closely enough. The effect was small, and estiamtes of theta and T_hat were unaffected or affected only very little, repsectively.
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r1115 | kevin | 2005-12-05 11:30:44 -0800 (Mon, 05 Dec 2005) | 2 lines
added #include <Sequence/Coalescent/DemographicModels.hpp>
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r1114 | kevin | 2005-12-05 11:30:19 -0800 (Mon, 05 Dec 2005) | 2 lines
fixed a bug where a deprecated function was used
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r1113 | kevin | 2005-12-05 11:29:52 -0800 (Mon, 05 Dec 2005) | 2 lines
defined constant SEQMAXDOUBLE
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r1112 | kevin | 2005-12-05 11:29:31 -0800 (Mon, 05 Dec 2005) | 2 lines
added constant SEQMAXDOUBLE
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r1111 | kevin | 2005-12-05 11:29:09 -0800 (Mon, 05 Dec 2005) | 2 lines
Added new header in Sequence/Coalescent that adds some functions for simple coalescent of common demographic scenarios. An example file (examples/bottleneck.cc) was also added.
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r1110 | kevin | 2005-12-05 07:47:38 -0800 (Mon, 05 Dec 2005) | 2 lines
Fixed bug in init_sample. Regions with 0 "sites" now have the last "site" in the chromosome labelled 0, which is correct. Previously, it was labelled 1.
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r1109 | kevin | 2005-11-11 07:03:09 -0800 (Fri, 11 Nov 2005) | 2 lines
added function double total_time_on_arg(...)
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r1108 | kevin | 2005-11-11 07:02:29 -0800 (Fri, 11 Nov 2005) | 2 lines
got rid of extraenous copying. code now cleaner, no use of malloc, and uses less overall memory
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r1106 | kevin | 2005-10-15 07:45:00 -0700 (Sat, 15 Oct 2005) | 2 lines
package 1.6.0
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r1105 | kevin | 2005-10-15 07:41:02 -0700 (Sat, 15 Oct 2005) | 3 lines
1.) functions needing an outgroup now return "nan" if it is not present
2.) fixed bug in calculating number of haplotypes for when there were no SNPs in the data and the object was constructed with a SimData object that is empty. A value of 0 was returned instead of 1.
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r1104 | kevin | 2005-10-10 15:19:38 -0700 (Mon, 10 Oct 2005) | 2 lines
operator== now declared as const (d'oh!), and operator!= now declared
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r1102 | kevin | 2005-09-20 11:52:02 -0700 (Tue, 20 Sep 2005) | 2 lines
listed changes
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r1101 | kevin | 2005-09-20 11:44:20 -0700 (Tue, 20 Sep 2005) | 2 lines
read and print now virtual functions
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r1100 | kevin | 2005-09-07 12:52:54 -0700 (Wed, 07 Sep 2005) | 2 lines
removed definition of deprecated member function fromstdin()
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r1099 | kevin | 2005-09-07 12:52:09 -0700 (Wed, 07 Sep 2005) | 2 lines
removed deprecated fromstdin() function.
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r1098 | kevin | 2005-08-25 06:37:12 -0700 (Thu, 25 Aug 2005) | 2 lines
readied files for releasing 1.5.9
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r1097 | kevin | 2005-08-24 08:08:13 -0700 (Wed, 24 Aug 2005) | 2 lines
now outputs total codon usage table at end of output
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r1096 | kevin | 2005-08-24 08:07:44 -0700 (Wed, 24 Aug 2005) | 2 lines
updated to match new interface to routines in Sequence/Coalescent/Mutation.hpp
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r1095 | kevin | 2005-08-24 08:05:03 -0700 (Wed, 24 Aug 2005) | 2 lines
much more efficient routines for putting coalescent simulation results into a SimData object
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r1094 | kevin | 2005-08-24 08:04:19 -0700 (Wed, 24 Aug 2005) | 2 lines
added function minimize_arg and class sfs_times
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r1093 | kevin | 2005-08-24 08:03:19 -0700 (Wed, 24 Aug 2005) | 2 lines
added more STL-like typedefs and updated member functions accordingly
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r1092 | kevin | 2005-08-24 07:57:33 -0700 (Wed, 24 Aug 2005) | 2 lines
The default constructor of PolyTable now takes two arguments--the sample size and # of snps. These can be used to make "blank" tables. The defaults are both 0, so a no-argument construction is still possible, maintaining syntax compatibility w/previous versions. The SimData class now takes advantage of this and is a big speedup when doing coalescent simulations.
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r1091 | kevin | 2005-08-24 07:51:15 -0700 (Wed, 24 Aug 2005) | 2 lines
members of struct marginal are now more STL-like
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r1090 | kevin | 2005-08-24 07:50:30 -0700 (Wed, 24 Aug 2005) | 2 lines
made member function declarations more STL-container-like
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r1089 | kevin | 2005-08-24 07:49:57 -0700 (Wed, 24 Aug 2005) | 2 lines
added typedefs and made member functions more STL-container-like (breaks binary compatibility)
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r1087 | kevin | 2005-07-29 06:57:57 -0700 (Fri, 29 Jul 2005) | 2 lines
package 1.5.8
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r1086 | kevin | 2005-07-29 06:57:19 -0700 (Fri, 29 Jul 2005) | 2 lines
undid the change in crossover() that appeared in 1.5.7 as it lead to massive RAM usage
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r1084 | kevin | 2005-07-19 13:56:26 -0700 (Tue, 19 Jul 2005) | 2 lines
package 1.5.7
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r1083 | kevin | 2005-07-19 13:53:37 -0700 (Tue, 19 Jul 2005) | 2 lines
handles all the examples now, for make clean
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r1082 | kevin | 2005-07-19 13:53:06 -0700 (Tue, 19 Jul 2005) | 2 lines
bug fixed in call to RemoveInvariantColumns which led to the exclusion of snps for data sets with no outgroup where there was a singleton in the first individual in the file
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r1081 | kevin | 2005-07-19 13:52:22 -0700 (Tue, 19 Jul 2005) | 2 lines
more efficient insertion of chromosomes into sample vector
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r1080 | kevin | 2005-06-15 10:25:05 -0700 (Wed, 15 Jun 2005) | 3 lines
added new example (examples/freerec.cc)
fixed documentation of examples for coalescent simulation
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r1079 | kevin | 2005-06-15 09:27:58 -0700 (Wed, 15 Jun 2005) | 2 lines
cleaned up doxygen code
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r1078 | kevin | 2005-06-15 09:27:19 -0700 (Wed, 15 Jun 2005) | 2 lines
function definitions were unecessarily verbose re: iterator type arguments. now changed, and match prototypes exactly
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r1077 | kevin | 2005-06-15 09:25:50 -0700 (Wed, 15 Jun 2005) | 2 lines
removed extraneous ;
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r1076 | kevin | 2005-06-15 09:25:24 -0700 (Wed, 15 Jun 2005) | 2 lines
cleaned up doxygen tags
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r1075 | kevin | 2005-06-15 09:23:22 -0700 (Wed, 15 Jun 2005) | 2 lines
removed some using declarations in favor of explicit namespace resolution. This makes definitions match declarations exactly, so doxygen has a better time.
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r1074 | kevin | 2005-06-15 09:21:44 -0700 (Wed, 15 Jun 2005) | 2 lines
operator() was mistakenly declared as SingleSub::SingleSub::operator(). now fixed. (How did the compiler not catch that?)
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r1073 | kevin | 2005-06-15 06:23:59 -0700 (Wed, 15 Jun 2005) | 2 lines
replaced using declarations with explicit namespace qualifiers
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r1071 | kevin | 2005-06-15 06:02:19 -0700 (Wed, 15 Jun 2005) | 2 lines
package 1.5.6
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r1070 | kevin | 2005-06-15 05:52:18 -0700 (Wed, 15 Jun 2005) | 2 lines
updated main page documentation about compiling the library
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r1069 | kevin | 2005-06-15 05:41:33 -0700 (Wed, 15 Jun 2005) | 2 lines
The function RemoveFixedOutgroupInsertions is no longer recursive
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r1067 | kevin | 2005-06-09 09:28:53 -0700 (Thu, 09 Jun 2005) | 2 lines
package 1.5.5
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r1066 | kevin | 2005-06-08 07:59:46 -0700 (Wed, 08 Jun 2005) | 2 lines
type of marginal::nsam changed from const int to mutable int
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r1065 | kevin | 2005-06-06 10:26:36 -0700 (Mon, 06 Jun 2005) | 2 lines
the non-const operator[] now sets non_const_access=true;
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r1064 | kevin | 2005-06-06 07:38:01 -0700 (Mon, 06 Jun 2005) | 2 lines
update doxygen tags
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r1063 | kevin | 2005-06-06 07:36:58 -0700 (Mon, 06 Jun 2005) | 2 lines
updated documentation re: how this library uses the NDEBUG symbol
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r1062 | kevin | 2005-06-06 07:36:06 -0700 (Mon, 06 Jun 2005) | 2 lines
now #includes <cmath>
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r1061 | kevin | 2005-06-06 07:35:39 -0700 (Mon, 06 Jun 2005) | 2 lines
declarations and definitions of Minrec removed, moved to PolySNP.cc/PolySIM.cc
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r1060 | kevin | 2005-06-06 07:35:11 -0700 (Mon, 06 Jun 2005) | 2 lines
implemented Minrec in this file, moving the implementation from Recombination.cc
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r1059 | kevin | 2005-06-06 07:34:32 -0700 (Mon, 06 Jun 2005) | 5 lines
Several chagnes:
1.) preprocessing is done automatically upon object construction. This fixes a bug in which certain functions needed preprocessing returned incorrect results
2.) A definition of Minrec is moved from Recombination.cc into this file, and the implementation is now non-recursive. Testing suggests that it is correct.
3.) an assert() statement is added to most functions, assert( rep->_preprocessed); Given that the class is non-copyable, this assertion should never be able to fail, but better safe than sorry when debugging
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r1058 | kevin | 2005-05-29 06:21:02 -0700 (Sun, 29 May 2005) | 2 lines
cleaned up doxygen tags
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r1057 | kevin | 2005-05-28 07:02:41 -0700 (Sat, 28 May 2005) | 2 lines
fixed declaration of instantiaion of Clustalw<Fasta> to be ansi/iso c++.
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r1055 | kevin | 2005-05-27 13:02:38 -0700 (Fri, 27 May 2005) | 2 lines
updated for package 1.5.4
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r1053 | kevin | 2005-05-27 12:54:32 -0700 (Fri, 27 May 2005) | 2 lines
fixed bug in fixed S version of infinite_sites_sim_data
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r1051 | kevin | 2005-05-27 07:59:25 -0700 (Fri, 27 May 2005) | 2 lines
oops--forgot to add
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r1049 | kevin | 2005-05-27 07:56:59 -0700 (Fri, 27 May 2005) | 2 lines
make clean now cleans everything
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r1048 | kevin | 2005-05-27 07:56:37 -0700 (Fri, 27 May 2005) | 2 lines
fixed bug in SimData versions of the infinite sites routine that caused segfaults due to reallocation of the gamete_storage_type object
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r1047 | kevin | 2005-05-25 15:23:21 -0700 (Wed, 25 May 2005) | 2 lines
added #include guards
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r1046 | kevin | 2005-05-25 15:23:03 -0700 (Wed, 25 May 2005) | 2 lines
fixed bug in documentation
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r1045 | kevin | 2005-05-23 14:54:09 -0700 (Mon, 23 May 2005) | 2 lines
updates to documentation
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r1044 | kevin | 2005-05-23 13:44:52 -0700 (Mon, 23 May 2005) | 2 lines
fixed bugs in doxygen tags
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r1043 | kevin | 2005-05-23 13:42:58 -0700 (Mon, 23 May 2005) | 2 lines
updated for randomShuffleAdaptor now being in namespace Sequence
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r1042 | kevin | 2005-05-23 13:42:06 -0700 (Mon, 23 May 2005) | 2 lines
placed in namespace Sequence now
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r1041 | kevin | 2005-05-23 13:33:32 -0700 (Mon, 23 May 2005) | 2 lines
these shouldn't be in the repository
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r1040 | kevin | 2005-05-23 13:32:22 -0700 (Mon, 23 May 2005) | 2 lines
updated to additions and deletions of source files
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r1039 | kevin | 2005-05-23 13:30:56 -0700 (Mon, 23 May 2005) | 2 lines
now independent of random number generator scheme
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r1038 | kevin | 2005-05-23 13:30:26 -0700 (Mon, 23 May 2005) | 2 lines
replaced a for_each with a for loop because the former would not compile on OS X using gcc 4 (why, dammit, why?)
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r1037 | kevin | 2005-05-23 13:29:07 -0700 (Mon, 23 May 2005) | 2 lines
removed checks for boost random number related headers
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r1036 | kevin | 2005-05-23 13:28:33 -0700 (Mon, 23 May 2005) | 2 lines
in my pro-GNU Scientific Library world view, these source files have been declared unmaintainable. See <Sequence/RNG/gsl_rng_wrappers.hpp>
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r1035 | kevin | 2005-05-23 13:27:04 -0700 (Mon, 23 May 2005) | 2 lines
updated examples to reflect removal of boost-based rng system.
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r1034 | kevin | 2005-05-23 12:05:22 -0700 (Mon, 23 May 2005) | 2 lines
removed--these are part of the old coalescent simulation code
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r1033 | kevin | 2005-05-22 18:20:37 -0700 (Sun, 22 May 2005) | 2 lines
added several assert statement, and added some typecasts to handle compiler warnings.
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r1032 | kevin | 2005-05-22 18:16:12 -0700 (Sun, 22 May 2005) | 2 lines
moved some doxygen tags to bits/Mutation.tcc
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r1031 | kevin | 2005-05-22 15:01:59 -0700 (Sun, 22 May 2005) | 2 lines
fixed a segfault in the handling of re-allocation of gamete_storage_type. It now only erases if string size is > number of segsites, else it resizes.
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r1030 | kevin | 2005-05-22 12:11:42 -0700 (Sun, 22 May 2005) | 2 lines
updates to Makefile to reflect deleted files. New examples added. Doxygen tags updated
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r1029 | kevin | 2005-05-22 12:10:39 -0700 (Sun, 22 May 2005) | 2 lines
removed and replaced by the new implementation of coalescent simulation in Sequence/Coalescent/*
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r1028 | kevin | 2005-05-18 16:13:37 -0700 (Wed, 18 May 2005) | 2 lines
new example file showing simple coalescent simulation
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r1027 | kevin | 2005-05-18 15:37:32 -0700 (Wed, 18 May 2005) | 2 lines
added new coalescent simulation machinery. marked old code as deprecated. also added classed to act as wrappers to gsl random number generation routines.
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r1026 | kevin | 2005-05-18 15:35:57 -0700 (Wed, 18 May 2005) | 2 lines
fixed bug in handling sites with sample size 1 or 0 after accounting for missing data
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r1024 | kevin | 2005-04-21 08:04:34 -0700 (Thu, 21 Apr 2005) | 2 lines
package 1.5.3
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r1023 | kevin | 2005-04-21 07:55:40 -0700 (Thu, 21 Apr 2005) | 2 lines
fixed bug in ThetaPi() for sites where all but 1 individual have missing data.
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r1022 | kevin | 2005-04-08 05:39:49 -0700 (Fri, 08 Apr 2005) | 2 lines
package 1.5.2
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r1021 | kevin | 2005-04-08 05:39:20 -0700 (Fri, 08 Apr 2005) | 2 lines
The fixes to process_windows were incomplete, so the code was still buggy. Now fixed, and tested.
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r1019 | kevin | 2005-04-05 16:50:01 -0700 (Tue, 05 Apr 2005) | 2 lines
package version 1.5.1
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r1018 | kevin | 2005-04-05 10:34:57 -0700 (Tue, 05 Apr 2005) | 2 lines
I discovered a bug when sliding a window along the physical sequence (i.e., as opposed to a window of a fixed # of segregating sites). When the jump size was less than the window size, windows were not overlapping. This is now fixed
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r1017 | kevin | 2005-03-17 07:14:21 -0800 (Thu, 17 Mar 2005) | 2 lines
simplified, and added more summ stats to the output
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r1016 | kevin | 2005-03-17 05:42:55 -0800 (Thu, 17 Mar 2005) | 2 lines
added ufs.cc to list of sources to compile
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r1015 | kevin | 2005-03-17 05:42:34 -0800 (Thu, 17 Mar 2005) | 2 lines
new example program -- calculate the unfolded site frequency spectrum from a FASTA file of aligned sequences
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r1014 | kevin | 2005-01-29 18:18:39 -0800 (Sat, 29 Jan 2005) | 2 lines
preprocessor macros written so that file compiles without any -DXXX directives
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r1013 | kevin | 2005-01-29 18:17:53 -0800 (Sat, 29 Jan 2005) | 2 lines
preprocessor macros are now written so that, in the absence of -D directives, ANSI/ISO C++ constructs are prefered by default. Source files are also update to use Sequence/Portability/StringStreams.hpp where applicable
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r1012 | kevin | 2005-01-29 18:16:04 -0800 (Sat, 29 Jan 2005) | 2 lines
ThetaH is now correct when monomorphic sites are in the polymorphism table
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r1011 | kevin | 2005-01-29 18:13:09 -0800 (Sat, 29 Jan 2005) | 2 lines
added Sequence/Portability/StringStreams.hpp to list of source files
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r1010 | kevin | 2005-01-29 18:12:07 -0800 (Sat, 29 Jan 2005) | 2 lines
new file to handle <sstream> vs. <stringstream> and to provides typedefs for those classes
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r1009 | kevin | 2005-01-29 18:11:08 -0800 (Sat, 29 Jan 2005) | 2 lines
changed assign(...) call to this->assign(...) so that dependent names are made explicit, allowing the code to be compiled with gcc 3.4
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r1007 | kevin | 2005-01-11 18:40:52 -0800 (Tue, 11 Jan 2005) | 2 lines
package 1.5.0
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r1006 | kevin | 2005-01-11 18:40:14 -0800 (Tue, 11 Jan 2005) | 2 lines
removed some commented out code
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r1005 | kevin | 2005-01-11 18:39:36 -0800 (Tue, 11 Jan 2005) | 2 lines
package 1.5.0
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r1004 | kevin | 2005-01-11 12:54:05 -0800 (Tue, 11 Jan 2005) | 3 lines
improved creation of nan using strtod for cases where summary statistics are undefined.
class PolySIM now returns 0 instead of nan for ThetaW when there are 0 segregating sites in the sample.
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r1003 | kevin | 2005-01-03 15:42:58 -0800 (Mon, 03 Jan 2005) | 2 lines
fixed variance calculations so that they are now unbiased estimates of sample variance, and compatible with GSL and R.
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r1000 | kevin | 2004-12-24 10:24:02 -0800 (Fri, 24 Dec 2004) | 2 lines
make clean now cleans everything
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r999 | kevin | 2004-12-24 10:23:46 -0800 (Fri, 24 Dec 2004) | 2 lines
added example source that had somehow been deleted (?)
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r998 | kevin | 2004-12-16 08:15:42 -0800 (Thu, 16 Dec 2004) | 2 lines
now includes <ieeefp.h> on systems that have it, so that calls to finite() will work.
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r996 | kevin | 2004-12-08 09:49:59 -0800 (Wed, 08 Dec 2004) | 2 lines
fixed implicit typename
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r995 | kevin | 2004-12-08 08:46:53 -0800 (Wed, 08 Dec 2004) | 2 lines
fixed bug in documentation for how ThetaPi is calculated
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r991 | kevin | 2004-12-03 06:22:32 -0800 (Fri, 03 Dec 2004) | 2 lines
updated
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r989 | kevin | 2004-12-03 05:40:16 -0800 (Fri, 03 Dec 2004) | 2 lines
fixed bug in HKA module. An index variable was incremented incorrectly, leading to undefined values of divergence time and relative Ne
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r987 | kevin | 2004-11-29 17:59:32 -0800 (Mon, 29 Nov 2004) | 2 lines
package 1.4.9
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r986 | kevin | 2004-11-29 17:57:19 -0800 (Mon, 29 Nov 2004) | 2 lines
fixed declaration of explicit instantiations for ClustalW<Fasta> and phylipData<Fasta>
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r985 | kevin | 2004-11-27 07:20:14 -0800 (Sat, 27 Nov 2004) | 2 lines
added class declaration to explicit instantiations of Clustalw<Fasta> and phylipData<Fasta>
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r984 | kevin | 2004-11-27 07:19:44 -0800 (Sat, 27 Nov 2004) | 2 lines
fixed an "implicit typename" that worked under gcc 3.3 but not 3.4
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r983 | kevin | 2004-11-27 07:19:11 -0800 (Sat, 27 Nov 2004) | 2 lines
removing ; after } enclosing namespace declaration. Caused compilation to fail w/gcc 3.4.4
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r982 | kevin | 2004-11-27 06:08:25 -0800 (Sat, 27 Nov 2004) | 2 lines
removed ; after bracket closing namespace Sequence
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r979 | kevin | 2004-11-03 14:07:33 -0800 (Wed, 03 Nov 2004) | 2 lines
package 1.4.8
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r978 | kevin | 2004-11-03 13:36:01 -0800 (Wed, 03 Nov 2004) | 2 lines
fixed major bug in calculation of dervied states. it is now correct
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r969 | kevin | 2004-10-06 14:00:48 -0700 (Wed, 06 Oct 2004) | 2 lines
package 1.4.7
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r967 | kevin | 2004-10-06 13:34:12 -0700 (Wed, 06 Oct 2004) | 2 lines
Wall's B statistics are now properly set to -1 if !(S>1)
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r956 | kevin | 2004-10-04 14:21:53 -0700 (Mon, 04 Oct 2004) | 2 lines
read() no removes columns w/no snps and throws and exception if the sample size != the value stated by the infile
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r955 | kevin | 2004-10-04 13:46:01 -0700 (Mon, 04 Oct 2004) | 2 lines
removed definitions of specializations of PolyTableSlice<SimData>, as they are no longer necessary
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r954 | kevin | 2004-10-04 13:43:21 -0700 (Mon, 04 Oct 2004) | 2 lines
when doing a window accross a physical distance, empty and "full" windows are now both stored, instead of just the "full" ones that have SNPs in them.
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r953 | kevin | 2004-10-04 13:41:26 -0700 (Mon, 04 Oct 2004) | 2 lines
removed declarations of specializations, as they are no longer necessary
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r952 | kevin | 2004-09-20 08:39:22 -0700 (Mon, 20 Sep 2004) | 2 lines
package version 1.4.6
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r951 | kevin | 2004-09-12 16:43:36 -0700 (Sun, 12 Sep 2004) | 2 lines
estimate of relative Ne of species 2 is now more robust to loci in species 1 with S=0.
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r950 | kevin | 2004-09-12 16:39:22 -0700 (Sun, 12 Sep 2004) | 2 lines
Updated intro section of reference documentation
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r949 | kevin | 2004-09-03 12:00:26 -0700 (Fri, 03 Sep 2004) | 2 lines
remove cerr debugging...
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r948 | kevin | 2004-09-03 11:57:22 -0700 (Fri, 03 Sep 2004) | 2 lines
fixed handling of invariant loci in species a in function calcHKA
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r947 | kevin | 2004-09-03 09:49:17 -0700 (Fri, 03 Sep 2004) | 2 lines
added more documentation for HKAresults struct
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r946 | kevin | 2004-08-29 16:35:01 -0700 (Sun, 29 Aug 2004) | 2 lines
implemented members sum() and sumSquares().