From 70e896a9e0eb7ef7db89dd2abe4c412c0c434480 Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@gmail.com>
Date: Sat, 1 Jun 2024 14:11:56 -0500
Subject: [PATCH] remove query sequence processing from computeAlignments
 reader_thread, as it is now done in worker_thread

---
 src/align/include/computeAlignments.hpp | 98 +++++--------------------
 1 file changed, 20 insertions(+), 78 deletions(-)

diff --git a/src/align/include/computeAlignments.hpp b/src/align/include/computeAlignments.hpp
index 54547eb9..1500644f 100644
--- a/src/align/include/computeAlignments.hpp
+++ b/src/align/include/computeAlignments.hpp
@@ -215,84 +215,26 @@ namespace align
               w.store(true);
           }
 
-          // reader picks up candidate alignments from input
-          auto reader_thread =
-              [&]() {
-                  //Parse query sequences
-                  for(const auto &fileName : param.querySequences)
-                  {
-//#define DEBUG true
-#ifdef DEBUG
-                      std::cerr << "INFO, align::Aligner::computeAlignments, parsing query sequences in file " << fileName << std::endl;
-#endif
-
-                      //Open mashmap output file
-                      std::ifstream mappingListStream(param.mashmapPafFile);
-                      std::string mappingRecordLine;
-                      MappingBoundaryRow currentRecord;
-
-                      seqiter::for_each_seq_in_file(
-                          fileName, {}, "", 
-                          [&](const std::string& qSeqId,
-                              const std::string& _seq) {
-                              ++total_seqs;
-
-                              uint64_t rank_mapping = 0;
-
-                              // copy our input into a shared ptr
-                              std::shared_ptr<std::string> seq(new std::string(_seq));
-                              // todo: offset_t is an 32-bit integer, which could cause problems
-                              skch::offset_t len = seq->length();
-                              // upper-case our input and make sure it's canonical DNA (for WFA)
-                              skch::CommonFunc::makeUpperCaseAndValidDNA((char*)seq->c_str(), len);
-                              // todo maybe this should change to some kind of unique pointer?
-                              // something where we can GC it when we're done aligning to it
-                              //std::string qSequence = seq;
-                              //std::cerr << seq << std::endl;
-
-                              //Check if all mapping records are processed already
-                              while(!mappingListStream.eof() && mappingRecordLine.empty()) {
-                                  //Read first record from mashmap output file during first iteration
-                                  std::getline(mappingListStream, mappingRecordLine);
-                              }
-
-                              if( !mappingRecordLine.empty() ) {
-                                  parseMashmapRow(mappingRecordLine, currentRecord);
-
-                                  //Check if mapping query id matches current query sequence id
-                                  if(currentRecord.qId == qSeqId)
-                                  {
-                                      //Queue up this query record
-                                      auto q = new seq_record_t(currentRecord, mappingRecordLine, seq);
-                                      q->currentRecord.rankMapping = rank_mapping++;
-                                      seq_queue.push(q);
-
-                                      //Check if more mappings have same query sequence id
-                                      while(std::getline(mappingListStream, mappingRecordLine))
-                                      {
-                                          parseMashmapRow(mappingRecordLine, currentRecord);
-
-                                          if(currentRecord.qId != qSeqId)
-                                          {
-                                              //Break the inner loop to read query sequence
-                                              break;
-                                          }
-                                          else
-                                          {
-                                              auto q = new seq_record_t(currentRecord, mappingRecordLine, seq);
-                                              q->currentRecord.rankMapping = rank_mapping++;
-                                              seq_queue.push(q);
-                                          }
-                                      }
-                                  }
-                              }
-                          });
-
-                      mappingListStream.close();
-
-                  }
-                  reader_done.store(true);
-              };
+		  // reader picks up candidate alignments from input
+		  auto reader_thread =
+			  [&]() {
+				  std::ifstream mappingListStream(param.mashmapPafFile);
+				  std::string mappingRecordLine;
+				  MappingBoundaryRow currentRecord;
+
+				  while (!mappingListStream.eof()) {
+					  std::getline(mappingListStream, mappingRecordLine);
+					  if (!mappingRecordLine.empty()) {
+						  parseMashmapRow(mappingRecordLine, currentRecord);
+						  total_alignment_length += currentRecord.qEndPos - currentRecord.qStartPos;
+						  auto q = new seq_record_t(currentRecord, mappingRecordLine, nullptr);
+						  seq_queue.push(q);
+					  }
+				  }
+
+				  mappingListStream.close();
+				  reader_done.store(true);
+			  };
 
           // helper to check if we're still aligning
           auto still_working =