Commit c28e1ce9 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.46.0+dfsg

parent 3861dc05

src/BUSData.h

+7 −2
Original line number Diff line number Diff line
@@ -18,6 +18,11 @@ struct BUSHeader { 
  std::string text;

  std::vector<BUSTranscript> transcripts;

  std::vector<std::vector<int32_t>> ecs;

  uint32_t version;

  uint32_t bclen;

  uint32_t umilen;

  BUSHeader() : version(0), bclen(0), umilen(0) {}



};



struct BUSData {
@@ -26,8 +31,8 @@ struct BUSData { 
  int32_t ec;

  uint32_t count;

  uint32_t flags;  



  BUSData() : barcode(0), UMI(0), ec(-1), count(0), flags(0) {}

  uint32_t pad;

  BUSData() : barcode(0), UMI(0), ec(-1), count(0), flags(0), pad(0) {}

};



uint64_t stringToBinary(const std::string &s, uint32_t &flag);

src/common.h

+1 −1
Original line number Diff line number Diff line 
#ifndef KALLISTO_COMMON_H

#define KALLISTO_COMMON_H



#define KALLISTO_VERSION "0.45.1"

#define KALLISTO_VERSION "0.46.0"



#include <string>

#include <vector>

src/main.cpp

+119 −2
Original line number Diff line number Diff line
@@ -600,6 +600,106 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) { 
 

}



bool ParseTechnology(const std::string &techstr, std::vector<BUSOptionSubstr> &values, std::vector<int> &files, std::vector<std::string> &errorList, std::vector<BUSOptionSubstr> &bcValues) {

  int lastIndex = 0; //the last place in the string a colon and punctuation was found

  int currValue = 1; //tells us the index of the three sequences needed barcode, umi, sequence

  vector<int> numbers; //stores the numbers in a pairs

  const char punctuationCompare = ',';

  const char colonCompare = ':';

  bool colon;

  bool duplicate = false;

  std::string stringVal;

  int val;



  for(int i = 1; i < techstr.length(); i++) {

    colon = false;

    if(techstr[i] == colonCompare) {

      colon = true;

    }



    if(techstr[i] == punctuationCompare || colon) {

      stringVal = techstr.substr(lastIndex, i-lastIndex);

      try {

        val = stoi(stringVal);

        numbers.push_back(val);

        if(numbers.size() == 1) {

          if(!files.empty()) {

            for(int j = 0; j < files.size(); j++) {

              if(val == files[j]) {

                duplicate = true;

                break;

              }

            }

            if(!duplicate) {

              files.push_back(val);

            } else {

              duplicate = false;

            }

          } else {

            files.push_back(val);

          }

        }

        lastIndex = i + 1;

      } catch(const std:: invalid_argument& ia) {

        errorList.push_back("Error: Invalid argument");

        return true;

      }



      if(colon) {

        if(numbers.size() != 3) {

          errorList.push_back("Error: Wrong number of pairs provided");

          return true;

        }

      }

    }

    if(numbers.size() == 3) {

      if(currValue == 1) {

        bcValues.push_back(BUSOptionSubstr(numbers[0], numbers[1], numbers[2]));

      } else {

        values.push_back(BUSOptionSubstr(numbers[0], numbers[1], numbers[2]));

      }

      numbers.clear();

    }

    if(colon) {

      currValue++;

    }

  }



  if (files.empty()) {

    errorList.push_back(std::string("Error: parsing technology string \"") + techstr + "\"");

    return true;

  }



  std::sort(files.begin(), files.end());

  for(int k = 0; k < files.size()-1; k++) {

    if(files[k]+1 != files[k+1]) {

      errorList.push_back("Error: files aren't correctly referenced");

      return true;

    }

  }



  stringVal = techstr.substr(lastIndex, techstr.length()-lastIndex);

  if(numbers.size() == 2) {

    try {

      val = stoi(stringVal);

      numbers.push_back(val);

      values.push_back(BUSOptionSubstr(numbers[0], numbers[1], numbers[2]));

      numbers.clear();  

    } catch(const std:: invalid_argument& ia) {

      errorList.push_back("Error: Invalid argument");

      return true;

    }

  } else {

    errorList.push_back("Error: Wrong number of pairs provided");

    return true;

  }

  if(currValue != 3) {

    errorList.push_back("Error: Wrong number of substrings provided");

    return true;

  }

  return false;

}





void ParseOptionsH5Dump(int argc, char **argv, ProgramOptions& opt) {

  int peek_flag = 0;
@@ -762,10 +862,27 @@ bool CheckOptionsBus(ProgramOptions& opt) { 
      busopt.umi = BUSOptionSubstr(0,6,16);

      busopt.bc.push_back(BUSOptionSubstr(0,0,6));

    } else {

      cerr << "Unknown technology: " << opt.technology << endl;

      vector<int> files;

      vector<BUSOptionSubstr> values;

      vector<BUSOptionSubstr> bcValues;

      vector<std::string> errorList;

      bool invalid = ParseTechnology(opt.technology, values, files, errorList, bcValues);

      if(!invalid) {

        busopt.nfiles = files.size(); 

        for(int i = 0; i < bcValues.size(); i++) {

          busopt.bc.push_back(bcValues[i]);

        }

        busopt.umi = values[0];

        busopt.seq = values[1];

      } else {

        for(int j = 0; j < errorList.size(); j++) {

          cerr << errorList[j] << endl;

        }

        cerr << "Unable to create technology: " << opt.technology << endl;

        ret = false;

      }

    }

  }



  if (ret && opt.files.size() %  opt.busOptions.nfiles != 0) {

    cerr << "Error: Number of files (" << opt.files.size() << ") does not match number of input files required by "