PercolatorAdapter has been changed by Timo reverted to proper parsing… #9
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…or feature set due to a lot of missing information (lost in mascotadapter)
… better (prep pin missing tho)
…protein-level FDRs
…asPrefix in getScanNumber_ of PercolatorAdapter
… of native idstring. Prefix was not right for parsing + a couple of couts for debugging
Owner
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Please remove the mac files |
mwalzer
requested changes
Apr 1, 2017
src/utils/COMETAdapter.cpp
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| // -------------------------------------------------------------------------- | ||
| // $Maintainer: Chris Bielow $ | ||
| // $Authors: Andreas Bertsch, Chris Bielow $ | ||
| // $Authors: Leon Bichmann, Andreas Bertsch, Chris Bielow $ |
| // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| // | ||
| // -------------------------------------------------------------------------- | ||
| // $Maintainer: Chris Bielow $ |
| // if scan number is not available, use the scan index | ||
| Size idx = 0; | ||
| if ((idx = it->hasPrefix("scan=")) != string::npos) | ||
| if ((idx = it->find("scan=")) != string::npos) |
Owner
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please pull the latest commits from origin, this was changed.
| break; | ||
| } | ||
| else if ((idx = it->hasPrefix("index=")) != string::npos) | ||
| else if ((idx = it->find("index=")) != string::npos) |
Owner
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please pull the latest commits from origin, this was changed.
| //id <tab> label <tab> scannr <tab> calcmass <tab> expmass <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM | ||
| void preparePin_(vector<PeptideIdentification>& peptide_ids, StringList& feature_set, std::string& enz, TextFile& txt, int min_charge, int max_charge) | ||
| { | ||
| std::cout << "number of features = " << feature_set.size() << "\n"; |
| String pout_decoy_file_proteins(temp_directory_body + txt_designator + "_decoy_pout_proteins.tab"); | ||
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| LOG_DEBUG << "Writing percolator input file." << endl; | ||
| LOG_DEBUG << "Writing percolator input file." << pin_file << endl; |
Owner
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This is quite redundant as the PIN files are not removed if debug level > 2
Owner
|
Would you please rephrase the PR description as it is unclear to me what you mean. I did not find any changes from @timosachsenberg - Also, I updated the idXML consumption for PercolatorAdapter, which some of them get undone by this PR. Please correct. |
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Fix/consensus map id map index order
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… of native idstring. Prefix was not right for parsing + a couple of couts for debugging