Merge branch 'release/0.7.3'

CMakeLists.txt

@@ -8,7 +8,7 @@ project(octopus)
 
 set(octopus_VERSION_MAJOR 0)
 set(octopus_VERSION_MINOR 7)
-set(octopus_VERSION_PATCH 2)
+set(octopus_VERSION_PATCH 3)
 set(octopus_VERSION_RELEASE "")
 
 # Generate list of compile commands.  This helps debugging and doesn't have a downside.

scripts/install.py

@@ -99,8 +99,14 @@ def is_centos(version=None):
     else:
         return False
 
-def download_file(url, file_name):
-    urllib.request.urlretrieve(url, str(file_name))
+def download_file(url, file_name, max_attempts=10):
+    try:
+        urllib.request.urlretrieve(url, str(file_name))
+    except:
+        if max_attempts > 1:
+            download_file(url, file_name, max_attempts - 1)
+        else:
+            raise
 
 def git_clone(project):
     call(['git', 'clone', project])

src/CMakeLists.txt

@@ -427,6 +427,8 @@ set(CORE_SOURCES
     core/csr/measures/mean_likelihood.cpp
     core/csr/measures/allele_mapping_quality.hpp
     core/csr/measures/allele_mapping_quality.cpp
+    core/csr/measures/phylogeny_posterior.hpp
+    core/csr/measures/phylogeny_posterior.cpp
 
     core/models/haplotype_likelihood_array.hpp
     core/models/haplotype_likelihood_array.cpp

src/basics/aligned_read.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "aligned_read.hpp"

src/basics/aligned_read.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef aligned_read_hpp

src/basics/aligned_template.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "aligned_template.hpp"

src/basics/aligned_template.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef aligned_template_hpp

src/basics/cigar_string.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "cigar_string.hpp"

src/basics/cigar_string.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef cigar_string_hpp

src/basics/contig_region.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef contig_region_hpp

src/basics/genomic_region.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef genomic_region_hpp

src/basics/mappable_reference_wrapper.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_reference_wrapper_hpp

src/basics/pedigree.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "pedigree.hpp"

src/basics/pedigree.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef pedigree_hpp

src/basics/phred.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef phred_hpp

src/basics/ploidy_map.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "ploidy_map.hpp"

src/basics/ploidy_map.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef ploidy_map_hpp

src/basics/read_pileup.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "read_pileup.hpp"

src/basics/read_pileup.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef read_pileup_hpp

src/basics/tandem_repeat.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "tandem_repeat.hpp"

src/basics/tandem_repeat.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef tandem_repeat_hpp

src/basics/trio.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "trio.hpp"

src/basics/trio.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef trio_hpp

src/concepts/comparable.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef comparable_hpp

src/concepts/equitable.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef equitable_hpp

src/concepts/indexed.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef indexed_hpp

src/concepts/mappable.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_hpp

src/concepts/mappable_range.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_ranges_hpp

src/config/common.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "common.hpp"

src/config/common.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef common_hpp

src/config/config.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "config.hpp"

src/config/config.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef config_hpp

src/config/octopus_vcf.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "octopus_vcf.hpp"
@@ -26,7 +26,7 @@ VcfHeader::Builder make_header_template()
     result.add_format("DP", "1", "Integer", "Read depth at this position for this sample");
     result.add_format("FT", "1", "String", "Sample genotype filter indicating if this genotype was 'called'");
     result.add_format("GQ", "1", "Integer", "Conditional genotype quality (phred-scaled)");
-    result.add_format("PS", "1", "String", "Phase set");
+    result.add_format("PS", "1", "Integer", "Phase set");
     result.add_format("PQ", "1", "Integer", "Phasing quality");
     result.add_format("MQ", "1", "Integer", "RMS mapping quality");
 

src/config/octopus_vcf.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef octopus_vcf_hpp

src/config/option_collation.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "option_collation.hpp"
@@ -2035,14 +2035,14 @@ boost::optional<std::size_t> get_max_genotype_combinations(const OptionMap& opti
 {
     if (options.count("max-genotype-combinations") == 1) {
         return as_unsigned("max-genotype-combinations", options);
-    } else if (is_fast_mode(options)) {
-        return 10'000;
     } else if (caller == "cell") {
         return 1'000;
+    } else if (is_fast_mode(options)) {
+        return 10'000;
     } else if (caller == "trio") {
-        return 1'000'000;
+        return 100'000;
     } else if (caller == "population") {
-        return 500'000;
+        return 100'000;
     } else {
         return boost::none;
     }
@@ -2272,6 +2272,11 @@ auto get_caller_type(const OptionMap& options, const std::vector<SampleName>& sa
     return get_caller_type(options, samples, get_pedigree(options, samples));
 }
 
+bool aggregate_annotations(const OptionMap& options)
+{
+    return options.at("aggregate-annotations").as<bool>();
+}
+
 std::unique_ptr<VariantCallFilterFactory>
 make_call_filter_factory(const ReferenceGenome& reference, ReadPipe& read_pipe, const OptionMap& options,
                          boost::optional<fs::path> temp_directory)
@@ -2342,6 +2347,7 @@ make_call_filter_factory(const ReferenceGenome& reference, ReadPipe& read_pipe,
                 auto annotations = get_requested_measure_annotations(options);
                 output_options.annotations.insert(std::begin(annotations), std::end(annotations));
             }
+            output_options.aggregate_allele_annotations = aggregate_annotations(options);
             result->set_output_options(std::move(output_options));
         }
     }

src/config/option_collation.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef option_collation_hpp

src/config/option_parser.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "option_parser.hpp"
@@ -752,6 +752,10 @@ OptionMap parse_options(const int argc, const char** argv)
      po::value<std::vector<std::string>>()->multitoken()->implicit_value(std::vector<std::string> {"active"}, "active")->composing(),
      "Annotations to write to final VCF")
 
+     ("aggregate-annotations",
+     po::bool_switch()->default_value(false),
+     "Aggregate all multi-value annotations into a single value")
+
     ("filter-vcf",
      po::value<fs::path>(),
      "Filter the given Octopus VCF without calling")

src/config/option_parser.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef option_parser_hpp

src/config/system.h.in

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef system_hpp

src/config/version.h.in

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef version_hpp

src/containers/mappable_block.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_block_hpp

src/containers/mappable_flat_multi_set.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_set_hpp

src/containers/mappable_flat_set.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_flat_set_hpp

src/containers/mappable_map.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef mappable_map_hpp

src/containers/matrix_map.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef matrix_map_hpp

src/containers/probability_matrix.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef probability_matrix_hpp

src/core/callers/caller.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "caller.hpp"

src/core/callers/caller.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef caller_hpp

src/core/callers/caller_builder.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "caller_builder.hpp"

src/core/callers/caller_builder.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef caller_builder_hpp

src/core/callers/caller_factory.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "caller_factory.hpp"

src/core/callers/caller_factory.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef caller_factory_hpp

src/core/callers/cancer_caller.cpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #include "cancer_caller.hpp"

src/core/callers/cancer_caller.hpp

@@ -1,4 +1,4 @@
-// Copyright (c) 2015-2020 Daniel Cooke
+// Copyright (c) 2015-2021 Daniel Cooke
 // Use of this source code is governed by the MIT license that can be found in the LICENSE file.
 
 #ifndef cancer_caller_hpp