From 21f96f2862ce0e3f23fbcb7306d9e8fe494fd37d Mon Sep 17 00:00:00 2001
From: Tobias Rausch <rauschtobi@gmail.com>
Date: Fri, 7 Jun 2024 11:39:39 +0200
Subject: [PATCH] optimize parsing

---
 src/gtf.h     | 16 ++++++++--------
 src/padlock.h | 51 +++++++++++++++++++++++++++++++++++----------------
 2 files changed, 43 insertions(+), 24 deletions(-)

diff --git a/src/gtf.h b/src/gtf.h
index 7a1b1eb..ff53663 100644
--- a/src/gtf.h
+++ b/src/gtf.h
@@ -89,12 +89,6 @@ namespace dicey {
     boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
     std::cout << '[' << boost::posix_time::to_simple_string(now) << "] " << "GTF feature parsing" << std::endl;
 
-    // Check gzip
-    if (!is_gz(c.gtfFile)) {
-      std::cerr << "GTF file is not gzipped!" << std::endl;
-      return 0;
-    }
-
     // Map IDs to integer
     typedef std::map<std::string, int32_t> TIdMap;
     TIdMap idMap;
@@ -103,9 +97,12 @@ namespace dicey {
     int32_t eid = 0;
 
     // Parse GTF
-    std::ifstream file(c.gtfFile.string().c_str(), std::ios_base::in | std::ios_base::binary);
+    std::ifstream file;
     boost::iostreams::filtering_streambuf<boost::iostreams::input> dataIn;
-    dataIn.push(boost::iostreams::gzip_decompressor());
+    if (is_gz(c.gtfFile)) {
+      file.open(c.gtfFile.string().c_str(), std::ios_base::in | std::ios_base::binary);
+      dataIn.push(boost::iostreams::gzip_decompressor(), 16*1024);
+    } else file.open(c.gtfFile.string().c_str(), std::ios_base::in);
     dataIn.push(file);
     std::istream instream(&dataIn);
     std::string gline;
@@ -215,6 +212,9 @@ namespace dicey {
 	}
       }
     }
+    dataIn.pop();
+    if (is_gz(c.gtfFile)) dataIn.pop();
+    file.close();
     return geneInfo.size();
   }
 
diff --git a/src/padlock.h b/src/padlock.h
index 53062ec..68c7fb3 100644
--- a/src/padlock.h
+++ b/src/padlock.h
@@ -182,29 +182,48 @@ namespace dicey
     typedef std::vector<GeneInfo> TGeneInfo;
     TGeneInfo geneInfo;
     parseGTF(c, gRegions, geneInfo);
-    
+
     // Load barcodes
     std::cout << '[' << boost::posix_time::to_simple_string(boost::posix_time::second_clock::local_time()) << "] " << "Load barcodes" << std::endl;
     uint32_t numBarcodes = 0;
     if (!numBarcodes) {
-      faidx_t* fai = fai_load(c.barcodes.string().c_str());
-      for(int32_t refIndex = 0; refIndex < faidx_nseq(fai); ++refIndex) {
-	int32_t seqlen;
-	char* seq = faidx_fetch_seq(fai, faidx_iseq(fai, refIndex), 0, 20, &seqlen);
-	if (seqlen != 20) {
-	  std::cerr << "Invalid barcode length! Should be 20bp." << std::endl;
-	  return 1;
-	}
-	if (numBarcodes < geneInfo.size()) {
-	  geneInfo[numBarcodes].barcode = boost::to_upper_copy(std::string(seq));
-	  geneInfo[numBarcodes].code = std::string(faidx_iseq(fai, refIndex));
+      // Open barcode file
+      std::ifstream barFile;
+      boost::iostreams::filtering_streambuf<boost::iostreams::input> dataIn;
+      if (is_gz(c.barcodes)) {
+	barFile.open(c.barcodes.string().c_str(), std::ios_base::in | std::ios_base::binary);
+	dataIn.push(boost::iostreams::gzip_decompressor(), 16*1024);
+      } else barFile.open(c.barcodes.string().c_str(), std::ios_base::in);
+      dataIn.push(barFile);
+      std::istream instream(&dataIn);
+      std::string line;
+      uint64_t lcount = 0;
+      std::string colcode;
+      std::string barcode;
+      while(std::getline(instream, line)) {
+	if (!line.empty()) {
+	  if (lcount % 2 == 0) {
+	    if (line[0] == '>') {
+	      if (line.at(line.length() - 1) == '\r' ) colcode = line.substr(1, line.length() - 2);
+	      else colcode = line.substr(1);
+	    }
+	  } else {
+	    if (line.at(line.length() - 1) == '\r' ) barcode = boost::to_upper_copy(line.substr(0, line.length() - 1));
+	    else barcode = boost::to_upper_copy(line);
+	    if (numBarcodes < geneInfo.size()) {
+	      geneInfo[numBarcodes].barcode = barcode;
+	      geneInfo[numBarcodes].code = colcode;
+	      ++numBarcodes;
+	    } else break;
+	  }
+	  ++lcount;
 	}
-	++numBarcodes;
-	free(seq);
       }
-      fai_destroy(fai);
+      dataIn.pop();
+      if (is_gz(c.barcodes)) dataIn.pop();
+      barFile.close();
     }
-    
+
     // Reference index
     csa_wt<> fm_index;  
     boost::filesystem::path op = c.genome.parent_path() / c.genome.stem();