[med-svn] [Git][med-team/hyphy][master] 5 commits: routine-update: New upstream version
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Oct 19 11:20:43 BST 2021
Nilesh Patra pushed to branch master at Debian Med / hyphy
Commits:
ad995bf0 by Nilesh Patra at 2021-10-19T10:07:13+00:00
routine-update: New upstream version
- - - - -
efc421d8 by Nilesh Patra at 2021-10-19T10:07:23+00:00
New upstream version 2.5.33+dfsg
- - - - -
49ec6958 by Nilesh Patra at 2021-10-19T10:07:33+00:00
Update upstream source from tag 'upstream/2.5.33+dfsg'
Update to upstream version '2.5.33+dfsg'
with Debian dir 7c83d9a0c52cd6359f0665da985fcbe33476d838
- - - - -
70e88627 by Nilesh Patra at 2021-10-19T10:07:33+00:00
routine-update: Standards-Version: 4.6.0
- - - - -
723d9eb9 by Nilesh Patra at 2021-10-19T10:07:52+00:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- − .travis.yml
- debian/changelog
- debian/control
- res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
- res/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
- res/TemplateBatchFiles/libv3/IOFunctions.bf
- res/TemplateBatchFiles/libv3/all-terms.bf
- res/TemplateBatchFiles/libv3/tasks/alignments.bf
Changes:
=====================================
.travis.yml deleted
=====================================
@@ -1,152 +0,0 @@
-# paste config here
-notifications:
- slack: veg-igem:rqQd95zjTuZoRNElekQx2CLf
- email:
- recipients:
- - steven at stevenweaver.org
- - spond at temple.edu
- on_success: change
- on_failure: always
-
-branches:
- only:
- - master
- - develop
-
-dist: xenial
-
-language: cpp
-os: linux
-
-compiler:
- - gcc
-script:
- - export OMP_NUM_THREADS=4
- - travis_wait 60 eval $envSpecificTest
-
-
-jobs:
- include:
- - os: linux
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-9
- - gcc-9
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-9" CC="gcc-9"; fi
- - cmake .
- - make
- env:
- - envSpecificTest="export PATH=$PATH:$(pwd); cd; git clone https://gitlab.com/rdvelazquez/testiphy.git; cd testiphy; ./testiphy HYPHYMP"
-
- - os: linux
- env:
- - envSpecificTest="make test"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-9
- - gcc-9
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-9" CC="gcc-9"; fi
- - cmake .
- - make
-
-
- # ---- Just run the hbl unit tests with gcc-4, 5 and 6 ----
- # gcc-4
- - os: linux
- env:
- - envSpecificTest="bash ./run_unit_tests.sh"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-4.9
- - gcc-4.9
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-4.9" CC="gcc-4.9"; fi
- - cmake .
- - make
-
- # gcc-5
- - os: linux
- env:
- - envSpecificTest="bash ./run_unit_tests.sh"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-5
- - gcc-5
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi
- - cmake .
- - make
-
- # gcc-6
- - os: linux
- env:
- - envSpecificTest="bash ./run_unit_tests.sh"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-6
- - gcc-6
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi
- - cmake .
- - make
- # gcc-7
- - os: linux
- env:
- - envSpecificTest="bash ./run_unit_tests.sh"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-7
- - gcc-7
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
- - cmake .
- - make
- # gcc-8
- - os: linux
- env:
- - envSpecificTest="bash ./run_unit_tests.sh"
- addons:
- apt:
- sources:
- - llvm-toolchain-precise
- - ubuntu-toolchain-r-test
- - george-edison55-precise-backports
- packages:
- - g++-8
- - gcc-8
- install:
- - if [ "$CXX" = "g++" ]; then export CXX="g++-8" CC="gcc-8"; fi
- - cmake .
- - make
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+hyphy (2.5.33+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Nilesh Patra <nilesh at debian.org> Tue, 19 Oct 2021 10:07:52 +0000
+
hyphy (2.5.32+dfsg-1) unstable; urgency=medium
* New upstream version 2.5.32+dfsg
=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
libsqlite3-dev,
pkg-config,
chrpath
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/hyphy
Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
Homepage: https://hyphy.org/
=====================================
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
=====================================
@@ -134,7 +134,7 @@ if (^"fel.ci") {
{"alpha", "Synonymous substitution rate at a site"}
{"beta", "Non-synonymous substitution rate at a site"}
{"alpha=beta", "The rate estimate under the neutral model"}
- {"LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"}
+ {"LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"}
{"p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"}
{"Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"}
{"dN/dS LB", "95% profile likelihood CI lower bound for dN/dS (if available)"}
@@ -148,7 +148,7 @@ if (^"fel.ci") {
fel.table_headers = {{"alpha", "Synonymous substitution rate at a site"}
{"beta", "Non-synonymous substitution rate at a site"}
{"alpha=beta", "The rate estimate under the neutral model"}
- {"LRT", "Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha"}
+ {"LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"}
{"p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"}
{"Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"}};
fel.table_screen_output = {{"Codon", "Partition", "alpha", "beta", "LRT", "Selection detected?"}};
@@ -406,7 +406,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
^"fel.beta_scaler_test" = 1;
^"fel.beta_scaler_nuisance" = 1;
-
Optimize (results, ^lf
, {
@@ -417,24 +416,27 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
);
- ci = None;
if (^"fel.ci") {
- if (^"fel.srv") {
- lf_stash = estimators.TakeLFStateSnapshot (lf);
- global omega_ratio_for_ci;
- if (^"fel.alpha_scaler" == 0.0) { // has no syn_variation
- ^"fel.alpha_scaler" = 1e-8;
- }
- omega_ratio_for_ci :< 10000;
- omega_ratio_for_ci :>0;
- omega_ratio_for_ci = ^"fel.beta_scaler_test" / ^"fel.alpha_scaler";
+ if (!sim_mode) {
+ if (^"fel.srv") {
+ lf_stash = estimators.TakeLFStateSnapshot (lf);
+ global omega_ratio_for_ci;
+ if (^"fel.alpha_scaler" == 0.0) { // has no syn_variation
+ ^"fel.alpha_scaler" = 1e-8;
+ }
+ omega_ratio_for_ci :< 10000;
+ omega_ratio_for_ci :>0;
+ omega_ratio_for_ci = ^"fel.beta_scaler_test" / ^"fel.alpha_scaler";
- ^"fel.beta_scaler_test" := omega_ratio_for_ci * ^"fel.alpha_scaler";
- ci = parameters.GetProfileCI (&omega_ratio_for_ci, lf, 0.95);
- estimators.RestoreLFStateFromSnapshot (lf, lf_stash);
- } else {
- ci = parameters.GetProfileCI ("fel.beta_scaler_test", lf, 0.95);
+ ^"fel.beta_scaler_test" := omega_ratio_for_ci * ^"fel.alpha_scaler";
+ ci = parameters.GetProfileCI (&omega_ratio_for_ci, lf, 0.95);
+ estimators.RestoreLFStateFromSnapshot (lf, lf_stash);
+ } else {
+ ci = parameters.GetProfileCI ("fel.beta_scaler_test", lf, 0.95);
+ }
}
+ } else {
+ ci = None;
}
if (sim_mode) {
@@ -456,8 +458,10 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
Null [utility.getGlobalValue("terms.fit.log_likelihood")] = results[1][0];
}
-
+
if (!sim_mode) {
+ tree_name = (lfInfo["Trees"])[0];
+ sum = (BranchLength (^tree_name, -1)*^"fel.selected_branches_index")[0];
if (^"fel.resample") {
N = ^"fel.resample";
sims = {};
@@ -474,12 +478,14 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod
is = fel.handle_a_site (lf, sims[i], partition_index, pattern_info, model_mapping, TRUE);
null_LRT[i] = is;
}
- return {utility.getGlobalValue("terms.alternative") : alternative, utility.getGlobalValue("terms.Null"): Null, utility.getGlobalValue("terms.simulated"): null_LRT};
+ return {utility.getGlobalValue("terms.alternative") : alternative, utility.getGlobalValue("terms.Null"): Null, utility.getGlobalValue("terms.simulated"): null_LRT, utility.getGlobalValue("terms.confidence_interval"): ci};
}
}
-
+
+
return {utility.getGlobalValue("terms.alternative") : alternative,
utility.getGlobalValue("terms.Null"): Null,
+ utility.getGlobalValue("terms.math.sum") : sum,
utility.getGlobalValue("terms.confidence_interval"): ci};
}
@@ -581,18 +587,21 @@ lfunction fel.store_results (node, result, arguments) {
} };
}
-
+ has_lrt = FALSE;
if (None != result) { // not a constant site
lrt = math.DoLRT ((result[utility.getGlobalValue("terms.Null")])[utility.getGlobalValue("terms.fit.log_likelihood")],
(result[utility.getGlobalValue("terms.alternative")])[utility.getGlobalValue("terms.fit.log_likelihood")],
1);
-
- if (result / ^"terms.simulated") {
+
+ has_lrt = result / ^"terms.simulated";
+
+ if (has_lrt) {
pv = +((result[^"terms.simulated"])["_MATRIX_ELEMENT_VALUE_>=" + lrt [utility.getGlobalValue("terms.LRT")]]);
lrt [utility.getGlobalValue("terms.p_value")] = (pv+1)/(1+^"fel.resample");
}
+
result_row [0] = estimators.GetGlobalMLE (result[utility.getGlobalValue("terms.alternative")], ^"fel.site_alpha");
result_row [1] = estimators.GetGlobalMLE (result[utility.getGlobalValue("terms.alternative")], ^"fel.site_beta");
result_row [2] = estimators.GetGlobalMLE (result[utility.getGlobalValue("terms.Null")], ^"fel.site_beta");
@@ -600,17 +609,19 @@ lfunction fel.store_results (node, result, arguments) {
result_row [4] = lrt [utility.getGlobalValue("terms.p_value")];
- sum = 0;
+
/*alternative_lengths = ((result[utility.getGlobalValue("terms.alternative")])[utility.getGlobalValue("terms.branch_length")])[0];
+
+ tname = utility.getGlobalValue("terms.tree_attributes.test");
+ for (_node_; in; ^"fel.case_respecting_node_names") {
+ _node_class_ = ((^"fel.selected_branches")[partition_index])[_node_];
+ if (_node_class_ == tname) {
+ sum += ((alternative_lengths)[_node_])[^"terms.fit.MLE"];
+ }
+ }*/
- utility.ForEach (^"fel.case_respecting_node_names", "_node_",
- '_node_class_ = ((^"fel.selected_branches")[`&partition_index`])[_node_];
- if (_node_class_ == utility.getGlobalValue("terms.tree_attributes.test")) {
- `&sum` += ((`&alternative_lengths`)[_node_])[utility.getGlobalValue("terms.fit.MLE")];
- }
- ');*/
-
- result_row [5] = sum;
+
+ result_row [5] = result[^"terms.math.sum"];
if (None != result [^"terms.confidence_interval"]) {
result_row [6] = (result [^"terms.confidence_interval"])[^"terms.lower_bound"];
@@ -621,13 +632,18 @@ lfunction fel.store_results (node, result, arguments) {
utility.EnsureKey (^"fel.site_results", partition_index);
+ if (has_lrt) {
+ utility.EnsureKey (^"fel.site_LRT", partition_index);
+ }
+
+ for (_fel_result_; in; pattern_info[utility.getGlobalValue("terms.data.sites")]) {
+ ((^"fel.site_results")[partition_index])[_fel_result_] = result_row;
+ fel.report.echo (_fel_result_, partition_index, result_row);
+ if (has_lrt) {
+ ((^"fel.site_LRT")[partition_index])[_fel_result_] = result[^"terms.simulated"];
+ }
+ }
- utility.ForEach (pattern_info[utility.getGlobalValue("terms.data.sites")], "_fel_result_",
- '
- (fel.site_results[`&partition_index`])[_fel_result_] = `&result_row`;
- fel.report.echo (_fel_result_, `&partition_index`, `&result_row`);
- '
- );
//assert (0);
@@ -635,6 +651,7 @@ lfunction fel.store_results (node, result, arguments) {
//----------------------------------------------------------------------------------------
fel.site_results = {};
+fel.site_LRT = {};
for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.partition_index += 1) {
fel.report.header_done = FALSE;
@@ -650,17 +667,22 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par
// beta = beta_scaler_test * branch_length or beta_nuisance_test * branch_length
SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);
+ fel.selected_branches_index = {1,utility.Array1D (fel.case_respecting_node_names)+1};
+ fel.i = 0;
for (_node_; in; fel.case_respecting_node_names) {
_node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
if (_node_class_ == terms.tree_attributes.test) {
+ fel.selected_branches_index [fel.i] = 1;
_beta_scaler = fel.scalers[1];
} else {
_beta_scaler = fel.scalers[2];
}
fel.apply_proportional_site_constraint ("fel.site_tree", _node_, fel.alpha, fel.beta, fel.scalers[0], _beta_scaler, (( fel.final_partitioned_mg_results[terms.branch_length])[fel.partition_index])[_node_]);
+ fel.i += 1;
}
-
+
+
/*
utility.ForEach (fel.case_respecting_node_names, "_node_",
'_node_class_ = (fel.selected_branches[fel.partition_index])[_node_];
@@ -695,7 +717,7 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par
fel.queue = mpi.CreateQueue ({"LikelihoodFunctions": {{"fel.site_likelihood"}},
"Models" : {{"fel.site.mg_rev"}},
"Headers" : {{"libv3/all-terms.bf","libv3/tasks/alignments.bf"}},
- "Variables" : {{"fel.srv","fel.resample","fel.ci"}}
+ "Variables" : {{"fel.srv","fel.resample","fel.ci","fel.selected_branches_index"}}
});
@@ -735,32 +757,35 @@ for (fel.partition_index = 0; fel.partition_index < fel.partition_count; fel.par
io.ClearProgressBar();
mpi.QueueComplete (fel.queue);
+
fel.partition_matrix = {Abs (fel.site_results[fel.partition_index]), Rows (fel.table_headers)};
-
- utility.ForEachPair (fel.site_results[fel.partition_index], "_key_", "_value_",
- '
+ for (_key_, _value_; in; fel.site_results[fel.partition_index]) {
for (fel.index = 0; fel.index < Rows (fel.table_headers); fel.index += 1) {
fel.partition_matrix [0+_key_][fel.index] = _value_[fel.index];
}
- '
- );
-
+ }
fel.site_results[fel.partition_index] = fel.partition_matrix;
-
}
fel.json [terms.json.MLE ] = {terms.json.headers : fel.table_headers,
terms.json.content : fel.site_results };
+if (fel.resample) {
+ (fel.json [terms.json.MLE ])[terms.LRT] = fel.site_LRT;
+}
io.ReportProgressMessageMD ("fel", "results", "** Found _" + fel.report.counts[0] + "_ sites under pervasive positive diversifying and _" + fel.report.counts[1] + "_ sites under negative selection at p <= " + fel.pvalue + "**");
selection.io.stopTimer (fel.json [terms.json.timers], "Total time");
selection.io.stopTimer (fel.json [terms.json.timers], "FEL analysis");
-if (fel.resamples) {
- fel.json [terms.simulated] = fel.resamples;
+if (fel.resample) {
+ fel.json [terms.simulated] = fel.resample;
+}
+
+if (fel.ci) {
+ fel.json [terms.confidence_interval] = TRUE;
}
GetString (_hpv,HYPHY_VERSION,0);
=====================================
res/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
=====================================
@@ -139,7 +139,6 @@ selection.io.startTimer (fubar.json [terms.json.timers], "Overall", 0);
fubar.path.base = (fubar.json [terms.json.input])[terms.json.file];
KeywordArgument ("cache", "Save FUBAR cache to [default is alignment+.FUBAR.cache]", fubar.path.base + ".FUBAR.cache");
-KeywordArgument ("output", "Save FUBAR results (JSON) to [default is alignment+.FUBAR.json]", fubar.codon_data_info[terms.data.file] + ".FUBAR.json");
/*------------------------------------------------------------------------------
@@ -149,6 +148,9 @@ KeywordArgument ("output", "Save FUBAR results (JSON) to [default is alignment
fubar.path.cache = io.PromptUserForString ("Save FUBAR cache to");
fubar.cache = io.LoadCacheFromFile (fubar.path.cache);
+KeywordArgument ("output", "Save FUBAR results (JSON) to [default is alignment+.FUBAR.json]", fubar.codon_data_info[terms.data.file] + ".FUBAR.json");
+fubar.codon_data_info [terms.json.json] = io.PromptUserForFilePath ("Save the resulting JSON file to");
+
fubar.table_output_options = {terms.table_options.header : TRUE, terms.table_options.minimum_column_width: 16, terms.table_options.align : "center"};
console.log ( "> FUBAR will write cache and result files to _`fubar.path.base`.FUBAR.cache_ and _`fubar.path.base`.FUBAR.json_, respectively \n\n");
=====================================
res/TemplateBatchFiles/libv3/IOFunctions.bf
=====================================
@@ -148,7 +148,7 @@ lfunction io.SpoolJSON(json, file) {
* @param file
*/
lfunction io.ParseJSON(file_path) {
- fscanf(file_path, "Raw", test);
+ fscanf(file_path, REWIND, "Raw", test);
parsed_test = Eval(test);
return parsed_test;
}
=====================================
res/TemplateBatchFiles/libv3/all-terms.bf
=====================================
@@ -30,6 +30,7 @@ namespace terms{
data_type = "datatype";
devnull = "/dev/null";
_namespace = "namespace";
+ warning = "warning";
category = "category";
mixture = "mixture";
=====================================
res/TemplateBatchFiles/libv3/tasks/alignments.bf
=====================================
@@ -335,6 +335,17 @@ function alignments.PromptForGeneticCodeAndAlignment(dataset_name, datafilter_na
return alignments.LoadCodonDataFile(dataset_name, datafilter_name, alignments.ReadCodonDataSet(dataset_name));
}
+/**
+ * Prompts user for genetic code and alignment; do not create error condition on stop codons
+ * @name alignments.PromptForGeneticCodeAndAlignmentWarnStops
+ * @param {String} dataset_name - the name of the dataset you wish to use
+ * @param {String} datafilter_name - the name of the dataset filter you wish to use
+ * @returns {Dictionary} r - metadata pertaining to the dataset
+ */
+function alignments.PromptForGeneticCodeAndAlignmentWarnStops (dataset_name, datafilter_name) {
+ return alignments.LoadCodonDataFileWarnStops(dataset_name, datafilter_name, alignments.ReadCodonDataSet(dataset_name));
+}
+
/**
* Loads genetic code and alignment from file path
* @name alignments.LoadGeneticCodeAndAlignment
@@ -393,6 +404,51 @@ function alignments.LoadCodonDataFile(dataset_name, datafilter_name, data_info)
return data_info;
}
+/**
+ * Creates codon dataset filter from data set; do not treat stop codons as an error condition
+ * @name alignments.LoadCodonDataFileWarnStops
+ * @param {String} datafilter_name - the name of the dataset filter you wish to use
+ * @param {String} dataset_name - the name of the existing dataset
+ * @param {Dictionary} data_info - DataSet metadata information
+ * @returns {Dictionary} updated data_info that includes the number of sites, dataset, and datafilter name
+ */
+function alignments.LoadCodonDataFileWarnStops(dataset_name, datafilter_name, data_info) {
+
+
+ DataSetFilter ^ datafilter_name = CreateFilter( ^ dataset_name, 3, , , data_info[terms.stop_codons]);
+
+ if (^"`datafilter_name`.sites"*3 != ^"`dataset_name`.sites") {
+ // generate a more diagnostic error here
+ data_info[^"terms.warning"] = {};
+
+ for (alignments.LoadCodonDataFile.i = 0; alignments.LoadCodonDataFile.i < ^"`dataset_name`.species"; alignments.LoadCodonDataFile.i += 1) {
+ DataSetFilter ^datafilter_name = CreateFilter( ^ dataset_name, 3, , "" + alignments.LoadCodonDataFile.i , data_info[terms.stop_codons]);
+ if (^"`datafilter_name`.sites"*3 != ^"`dataset_name`.sites") {
+ alignments.LoadCodonDataFile.name = alignments.GetIthSequenceOriginalName (dataset_name, alignments.LoadCodonDataFile.i);
+
+ alignments.LoadCodonDataFile.site_map = ^"`datafilter_name`.site_map";
+
+ alignments.LoadCodonDataFile.annotation_string = utility.PopulateDict (0, ^"`dataset_name`.sites",
+ '(alignments.LoadCodonDataFile.name[terms.data.sequence])[_idx]',
+ '_idx');
+
+
+ utility.ForEach (alignments.LoadCodonDataFile.site_map, "_value_",
+ '
+ `&alignments.LoadCodonDataFile.annotation_string`[_value_] = `&alignments.LoadCodonDataFile.annotation_string`[_value_] && 0;
+ ');
+
+ (data_info[^"terms.warning"])[alignments.LoadCodonDataFile.name[terms.id]] = Join ("",alignments.LoadCodonDataFile.annotation_string);
+ }
+ }
+ DataSetFilter ^ datafilter_name = CreateFilter( ^ dataset_name, 3, , , data_info[terms.stop_codons]);
+ }
+ data_info[terms.data.sites] = ^ "`datafilter_name`.sites";
+ data_info[terms.data.dataset] = dataset_name;
+ data_info[terms.data.datafilter] = datafilter_name;
+ return data_info;
+}
+
/**
* Creates nucleotide dataset filter from file
* @name alignments.ReadNucleotideAlignment
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/56826e5714bca2b37ee3c510b06dcb0a387781fb...723d9eb927a404b4fb43e0a48a6e0ed5adec28c3
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