debian/changelog

+kallisto (0.46.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Wed, 07 Aug 2019 13:01:05 +0200
+
 kallisto (0.45.1+dfsg-1) unstable; urgency=medium
 
   * Initial release (Closes: #925417)

debian/compat

-12

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                libhdf5-dev,
                libhts-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/kallisto
 Vcs-Git: https://salsa.debian.org/med-team/kallisto.git
 Homepage: https://pachterlab.github.io/kallisto

src/BUSData.h

@@ -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

 #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

@@ -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 "