From 17f709bd4c281fb63fb4b3060c3cd3644b056e5f Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 23 Nov 2023 09:15:37 -0600 Subject: [PATCH 1/2] disaple ties dropping for now --- .vscode/settings.json | 70 ++++++++++++++++++++++++++++++++++++ src/interface/parse_args.hpp | 4 +-- 2 files changed, 72 insertions(+), 2 deletions(-) create mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..904d21ff --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,70 @@ +{ + "files.associations": { + "array": "cpp", + "atomic": "cpp", + "bit": "cpp", + "*.tcc": "cpp", + "bitset": "cpp", + "cctype": "cpp", + "charconv": "cpp", + "chrono": "cpp", + "clocale": "cpp", + "cmath": "cpp", + "compare": "cpp", + "concepts": "cpp", + "condition_variable": "cpp", + "cstdarg": "cpp", + "cstddef": "cpp", + "cstdint": "cpp", + "cstdio": "cpp", + "cstdlib": "cpp", + "cstring": "cpp", + "ctime": "cpp", + "cwchar": "cpp", + "cwctype": "cpp", + "deque": "cpp", + "list": "cpp", + "map": "cpp", + "set": "cpp", + "string": "cpp", + "unordered_map": "cpp", + "unordered_set": "cpp", + "vector": "cpp", + "exception": "cpp", + "algorithm": "cpp", + "functional": "cpp", + "iterator": "cpp", + "memory": "cpp", + "memory_resource": "cpp", + "numeric": "cpp", + "random": "cpp", + "ratio": "cpp", + "string_view": "cpp", + "system_error": "cpp", + "tuple": "cpp", + "type_traits": "cpp", + "utility": "cpp", + "fstream": "cpp", + "initializer_list": "cpp", + "iomanip": "cpp", + "iosfwd": "cpp", + "iostream": "cpp", + "istream": "cpp", + "limits": "cpp", + "mutex": "cpp", + "new": "cpp", + "numbers": "cpp", + "ostream": "cpp", + "semaphore": "cpp", + "sstream": "cpp", + "stdexcept": "cpp", + "stop_token": "cpp", + "streambuf": "cpp", + "thread": "cpp", + "cinttypes": "cpp", + "typeinfo": "cpp", + "valarray": "cpp", + "codecvt": "cpp", + "shared_mutex": "cpp" + } +} \ No newline at end of file diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index 986189c9..432896f6 100644 --- a/src/interface/parse_args.hpp +++ b/src/interface/parse_args.hpp @@ -86,7 +86,7 @@ void parse_args(int argc, args::Flag drop_low_map_pct_identity(mapping_opts, "K", "drop mappings with estimated identity below --map-pct-id=%", {'K', "drop-low-map-id"}); args::Flag no_filter(mapping_opts, "MODE", "disable mapping filtering", {'f', "no-filter"}); args::ValueFlag map_sparsification(mapping_opts, "FACTOR", "keep this fraction of mappings", {'x', "sparsify-mappings"}); - args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"}); + //ToFix: args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"}); args::ValueFlag sketch_size(mapping_opts, "N", "sketch size for sketching.", {'w', "sketch-size"}); args::ValueFlag kmer_complexity(mapping_opts, "F", "Drop segments w/ predicted kmer complexity below this cutoff. Kmer complexity defined as #kmers / (s - k + 1)", {'J', "kmer-complexity"}); args::Flag no_hg_filter(mapping_opts, "", "Don't use the hypergeometric filtering and instead use the MashMap2 first pass filtering.", {'1', "no-hg-filter"}); @@ -352,7 +352,7 @@ void parse_args(int argc, align_parameters.sam_format = args::get(sam_format); align_parameters.no_seq_in_sam = args::get(no_seq_in_sam); map_parameters.split = !args::get(no_split); - map_parameters.dropRand = !args::get(keep_ties); + map_parameters.dropRand = false;//ToFix: !args::get(keep_ties); align_parameters.split = !args::get(no_split); map_parameters.mergeMappings = !args::get(no_merge); From d28e3d51bee8812b44a7c164c9dd26bca218d388 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 23 Nov 2023 09:16:27 -0600 Subject: [PATCH 2/2] cleaning --- .vscode/settings.json | 70 ------------------------------------------- 1 file changed, 70 deletions(-) delete mode 100644 .vscode/settings.json diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index 904d21ff..00000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,70 +0,0 @@ -{ - "files.associations": { - "array": "cpp", - "atomic": "cpp", - "bit": "cpp", - "*.tcc": "cpp", - "bitset": "cpp", - "cctype": "cpp", - "charconv": "cpp", - "chrono": "cpp", - "clocale": "cpp", - "cmath": "cpp", - "compare": "cpp", - "concepts": "cpp", - "condition_variable": "cpp", - "cstdarg": "cpp", - "cstddef": "cpp", - "cstdint": "cpp", - "cstdio": "cpp", - "cstdlib": "cpp", - "cstring": "cpp", - "ctime": "cpp", - "cwchar": "cpp", - "cwctype": "cpp", - "deque": "cpp", - "list": "cpp", - "map": "cpp", - "set": "cpp", - "string": "cpp", - "unordered_map": "cpp", - "unordered_set": "cpp", - "vector": "cpp", - "exception": "cpp", - "algorithm": "cpp", - "functional": "cpp", - "iterator": "cpp", - "memory": "cpp", - "memory_resource": "cpp", - "numeric": "cpp", - "random": "cpp", - "ratio": "cpp", - "string_view": "cpp", - "system_error": "cpp", - "tuple": "cpp", - "type_traits": "cpp", - "utility": "cpp", - "fstream": "cpp", - "initializer_list": "cpp", - "iomanip": "cpp", - "iosfwd": "cpp", - "iostream": "cpp", - "istream": "cpp", - "limits": "cpp", - "mutex": "cpp", - "new": "cpp", - "numbers": "cpp", - "ostream": "cpp", - "semaphore": "cpp", - "sstream": "cpp", - "stdexcept": "cpp", - "stop_token": "cpp", - "streambuf": "cpp", - "thread": "cpp", - "cinttypes": "cpp", - "typeinfo": "cpp", - "valarray": "cpp", - "codecvt": "cpp", - "shared_mutex": "cpp" - } -} \ No newline at end of file