#include <string>#include <vector>#include <set>#include <objmgr/object_manager.hpp>#include <objmgr/scope.hpp>#include <objmgr/seq_entry_handle.hpp>#include <objmgr/bioseq_ci.hpp>#include <objmgr/seq_vector.hpp>#include <objmgr/util/sequence.hpp>#include <algo/winmask/win_mask_util.hpp>
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Functions | |
| void | CheckDuplicates (const vector< string > &input, const string &infmt, const CWinMaskUtil::CIdSet *ids, const CWinMaskUtil::CIdSet *exclude_ids) |
| Check for possibly duplicate sequences in the input. More... | |
Function Documentation
◆ CheckDuplicates()
| void CheckDuplicates | ( | const vector< string > & | input, |
| const string & | infmt, | ||
| const CWinMaskUtil::CIdSet * | ids, | ||
| const CWinMaskUtil::CIdSet * | exclude_ids | ||
| ) |
Check for possibly duplicate sequences in the input.
input contains the list of input file names. The files should be in the fasta format. The function checks the input sequences for duplication and reports possible duplicates to the standard error.
- Parameters
-
input list of input file names infmt input format ids set of ids to check exclude_ids set of ids to ignore
Definition at line 535 of file win_mask_dup_table.cpp.
References dup_lookup_table::sample::begin(), CWinMaskUtil::consider(), data, CBioseq_Handle::eCoding_Iupac, eGetId_Best, dup_lookup_table::sample::end(), CBioseq_Handle::GetBioseqLength(), GetId(), CObjectManager::GetInstance(), CSeq_id::GetLabel(), CBioseq_Handle::GetSeqVector(), i, input(), MIN_SEQ_LENGTH, om, SAMPLE_LENGTH, SAMPLE_SKIP, and table.
Referenced by CWinMaskCountsGenerator::operator()().
