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Merged
sarahet merged 5 commits into from
May 9, 2023
Merged

Using less space during construction #211

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7c85a9b
fix: update to newest fmindex_collection
SGSSGene Apr 25, 2023
ed7a5a2
Update src/mkindex_algo.hpp
SGSSGene Apr 26, 2023
7b08976
fix: update fmindex_collection submodule
SGSSGene May 3, 2023
3270a47
update fmindex_collection submodule
SGSSGene May 5, 2023
d8286ae
[test] update test files
h-2 May 8, 2023
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2 changes: 1 addition & 1 deletion src/mkindex_algo.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -603,7 +603,7 @@ auto generateIndex(TStringSet & seqs, LambdaIndexerOptions const & options)
myPrint(options, 1, "Generating Index...");
double s = sysTime();

TIndex index{seqs | bio::views::to_rank | fmindex_collection::add_sentinels, 5};
TIndex index{seqs | bio::views::to_rank | fmindex_collection::add_sentinels, /*samplingRate*/ 5, options.threads};

double e = sysTime() - s;
myPrint(options, 1, " done.\n");
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4 changes: 1 addition & 3 deletions src/search_algo.hpp
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Expand Up @@ -470,11 +470,9 @@ inline void search_impl(LocalDataHolder<TGlobalHolder> & lH, TSeed && seed)
{
if constexpr (TGlobalHolder::c_dbIndexType == DbIndexType::FM_INDEX)
{
//!TODO a reversed FMIndex is used, so the query need to be reversed, so we search from left to right
// This is a conceptual TODO for fmindex_collection library
fmindex_collection::search_backtracking_with_buffers::search(
lH.gH.indexFile.index,
seed | std::views::reverse | bio::views::to_rank | fmindex_collection::add_sentinel,
seed | bio::views::to_rank | fmindex_collection::add_sentinel,
lH.searchOpts.maxSeedDist,
lH.cursor_tmp_buffer,
lH.cursor_tmp_buffer2,
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2 changes: 1 addition & 1 deletion submodules/fmindex-collection
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Submodule fmindex-collection updated 105 files
18 changes: 9 additions & 9 deletions test/data/datasources.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ include (cmake/app_datasources.cmake)

## Index input files

set(BASEURL "https://github.com/h-2/lambda-testdata/646b6fc570c5b3673fde6819ea983159921c0360")
set(BASEURL "https://github.com/h-2/lambda-testdata/0a52e3bed1daf8646a496b63721b912fef3364bd")

declare_datasource (FILE db_nucl.fasta.gz
URL ${BASEURL}/input_files/db_nucl.fasta.gz
Expand All @@ -22,35 +22,35 @@ declare_datasource (FILE db_prot.fasta.gz

declare_datasource (FILE db_nucl_fm.fasta.gz.lba
URL ${BASEURL}/output_files/db_nucl_fm.fasta.gz.lba
URL_HASH SHA256=7a139ea6d9da493ae80a1b0de0060f018cc408ce5b130496320b7f18b6f43eda)
URL_HASH SHA256=68de7b2822b3f47268efee8becd400697cb1581a7055d1b581af365dd27f7a89)

declare_datasource (FILE db_nucl_bifm.fasta.gz.lba
URL ${BASEURL}/output_files/db_nucl_bifm.fasta.gz.lba
URL_HASH SHA256=4bc3894485ac11210149cb29cbc7a04ec3e8f01d1cc55d50b7c15e61d1a0c115)
URL_HASH SHA256=e812f75f1672b5dc4b8cb6078ce209ec809d21783424836ccbe0c9b78f37887c)

declare_datasource (FILE db_nucl_bs_fm.fasta.gz.lba
URL ${BASEURL}/output_files/db_nucl_bs_fm.fasta.gz.lba
URL_HASH SHA256=e7429e16fa79114228a42e367843719f8bf56374c32537a5c25e5c9a062f3faf)
URL_HASH SHA256=b17d4e29f424af54fa802344ae9d4af974dbfc16d0445741e08de6f3cfface0b)

declare_datasource (FILE db_nucl_bs_bifm.fasta.gz.lba
URL ${BASEURL}/output_files/db_nucl_bs_bifm.fasta.gz.lba
URL_HASH SHA256=dae02a72f5dd40ccb67f8c4fc8f84b04d148074f84e5e088fff0e61e7c2cda99)
URL_HASH SHA256=6dc216251505f0a913dffb9dc97699898492d511934dbcd1c9961337a151a62b)

declare_datasource (FILE db_prot_fm.fasta.gz.lba
URL ${BASEURL}/output_files/db_prot_fm.fasta.gz.lba
URL_HASH SHA256=cc9a563f5a2a2e7fe27b9d19761e8326371625dadf2509289b7a52df65b31da3)
URL_HASH SHA256=57fa7a4319c5eb4dded850a79beefa1c5eca6927c91541cd7d658fde0ab7d166)

declare_datasource (FILE db_prot_bifm.fasta.gz.lba
URL ${BASEURL}/output_files/db_prot_bifm.fasta.gz.lba
URL_HASH SHA256=0b2cdbea634481efb840c901ed768bc9bc2811ac87f16cca751c327094c50c75)
URL_HASH SHA256=76d0405235aff8145fe0d90399ffb7d3619ad2fedc37776771a1ca8a38b79a5d)

declare_datasource (FILE db_trans_fm.fasta.gz.lba
URL ${BASEURL}/output_files/db_trans_fm.fasta.gz.lba
URL_HASH SHA256=49c0b6784df6de0d6e064c65d034ad3ced961283135f5cc14b86b1048059a0c9)
URL_HASH SHA256=dc94a97d19a2ad224b995640bcacfc8fb6c7aa87ef134f3e61647c5b31286696)

declare_datasource (FILE db_trans_bifm.fasta.gz.lba
URL ${BASEURL}/output_files/db_trans_bifm.fasta.gz.lba
URL_HASH SHA256=172f3fb7c529bcf1eff086238efa1c66ce9a609c7abf6146105fa243c3cfcc4d)
URL_HASH SHA256=3ffce0f1115888bce562460e7f4f1222af7052cd8a85a32db0813eac317d8be5)

## Query input files

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