removed uses of assert from c++ code

mritchielab · Jul 10, 2023 · ae50f71 · ae50f71
1 parent 7bb5009
commit ae50f71
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Showing 6 changed files with 103 additions and 99 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -20,6 +20,7 @@ export(sc_annotate_plots)
 export(sc_long_multisample_pipeline)
 export(sc_long_pipeline)
 export(sc_mutations)
+export(testfuncR)
 import(zlibbioc)
 importFrom(BiocGenerics,cbind)
 importFrom(BiocGenerics,colnames)

diff --git a/src/main-functions/group_bam2isoform.cpp b/src/main-functions/group_bam2isoform.cpp
@@ -36,96 +36,96 @@ struct DataStruct2 {
 static std::unordered_map<std::string, std::string> 
 get_fa_dict(std::string filename)
 {
- // // Modify in place
- // auto
- // string_toupper = [] (std::string &input)
- // { std::transform(input.begin(), input.end(), input.begin(), [](unsigned char c) { return std::toupper(c); }); };
-
- // std::string ch = "";
- // std::stringstream sequence;
- // std::unordered_map<std::string, std::string> output;
-
- // std::ifstream infile(filename);
-
- // std::string line;
- // while (std::getline(infile, line)) {
- //  if (line[0] == '>') {
- //  if (ch != "") {
- //  output[ch] = sequence.str();
- //  }
- //  ch = strip(std::string(line.begin()+1, line.end()));
- //  string_toupper(ch);
- //  sequence.str(""); // reset the stringstream to empty
- //  } else {
- //  string_toupper(line);
- //  sequence << strip(line);
- //  }
- // }
- // infile.close();
+ // Modify in place
+ auto
+ string_toupper = [] (std::string &input)
+ { std::transform(input.begin(), input.end(), input.begin(), [](unsigned char c) { return std::toupper(c); }); };
+
+ std::string ch = "";
+ std::stringstream sequence;
+ std::unordered_map<std::string, std::string> output;
+
+ std::ifstream infile(filename);
+
+ std::string line;
+ while (std::getline(infile, line)) {
+ if (line[0] == '>') {
+ if (ch != "") {
+ output[ch] = sequence.str();
+ }
+ ch = strip(std::string(line.begin()+1, line.end()));
+ string_toupper(ch);
+ sequence.str(""); // reset the stringstream to empty
+ } else {
+ string_toupper(line);
+ sequence << strip(line);
+ }
+ }
+ infile.close();
 
- // return output;
+ return output;
 }
 
 static std::vector<StartEndPair>
 get_blocks(const BAMRecord &record) {
- // std::vector<StartEndPair> blocks;
- // int pos = record.reference_start;
-
- // for (const auto & [op, len] : record.cigar) {
- //  if ((op == BAM_CMATCH) ||
- //  (op == BAM_CEQUAL) ||
- //  (op == BAM_CDIFF)) {
- //  // add it to the blocks and move on
- //  blocks.push_back({pos, pos + len});
- //  pos += len;
- //  } else if (
- //  (op == BAM_CDEL) ||
- //  (op == BAM_CREF_SKIP)) {
- //  // just skip over this position
- //  pos += len;
- //  }
- // }
+ std::vector<StartEndPair> blocks;
+ int pos = record.reference_start;
+
+ for (const auto & [op, len] : record.cigar) {
+ if ((op == BAM_CMATCH) ||
+ (op == BAM_CEQUAL) ||
+ (op == BAM_CDIFF)) {
+ // add it to the blocks and move on
+ blocks.push_back({pos, pos + len});
+ pos += len;
+ } else if (
+ (op == BAM_CDEL) ||
+ (op == BAM_CREF_SKIP)) {
+ // just skip over this position
+ pos += len;
+ }
+ }
 
- // return blocks;
+ return blocks;
 }
 
 void 
 merge_files_and_delete(std::ofstream &outfile, const std::vector<std::string> &infiles) {
- // for (const auto &file : infiles) {
- //  std::ifstream infile(file);
+ for (const auto &file : infiles) {
+ std::ifstream infile(file);
 
- //  if (!infile.is_open()) continue;
+ if (!infile.is_open()) continue;
 
- //  std::string line;
- //  while (std::getline(infile, line)) {
- //  outfile << line;
- //  }
- //  infile.close();
+ std::string line;
+ while (std::getline(infile, line)) {
+ outfile << line;
+ }
+ infile.close();
 
- //  std::remove(file.c_str());
- // }
+ std::remove(file.c_str());
+ }
 }
 
 static int
 bam2isoform_fetch_function(const bam1_t *b, void *data)
 {
- // // retrieve the data from htslib and void * object
- // DataStruct2 *data_struct = (DataStruct2 *)data;
- // BAMRecord rec = read_record(b, data_struct->header);
+ // retrieve the data from htslib and void * object
+ DataStruct2 *data_struct = (DataStruct2 *)data;
+ BAMRecord rec = read_record(b, data_struct->header);
 
- // // smooth and update the CIGAR
- // std::vector<CigarPair> cigar = smooth_cigar(rec.cigar, 20);
- // rec.cigar = cigar;
- // rec.cigar_string = generate_cigar(cigar);
+ // smooth and update the CIGAR
+ std::vector<CigarPair> cigar = smooth_cigar(rec.cigar, 20);
+ rec.cigar = cigar;
+ rec.cigar_string = generate_cigar(cigar);
 
- // std::vector<StartEndPair> tmp_blocks = get_blocks(rec);
- // Junctions junctions = blocks_to_junctions(tmp_blocks);
+ std::vector<StartEndPair> tmp_blocks = get_blocks(rec);
+ Junctions junctions = blocks_to_junctions(tmp_blocks);
 
- // std::vector<std::string> tmp_blocks_str = ranges::map<StartEndPair, std::string>(tmp_blocks, [](StartEndPair sep) -> std::string { return sep.getString(); });
+ std::vector<std::string> tmp_blocks_str = ranges::map<StartEndPair, std::string>(tmp_blocks, [](StartEndPair sep) -> std::string { return sep.getString(); });
 
- // data_struct->isoform->add_isoform(junctions, rec.flag.read_reverse_strand);
- // data_struct->i = data_struct->i + 1;
- // return 0;
+ data_struct->isoform->add_isoform(junctions, rec.flag.read_reverse_strand);
+ data_struct->i = data_struct->i + 1;
+ return 0;
 }
 
 void group_bam2isoform(
@@ -141,11 +141,11 @@ void group_bam2isoform(
  const std::string &raw_gff3)
 {
  // random seed stuff here
- if (!file_exists(bam_in + ".bai")) {
- // Rcpp::stop("Can not find corresponding .bai file %s. Cancelling group_bam2isoform.\n", bam_in);
- Rcpp::Rcout << "Can not find corresponding .bai file " << bam_in << ". Cancelling group_bam2isoform.\n";
- return;
- }
+ // if (!file_exists(bam_in + ".bai")) {
+ //  // Rcpp::stop("Can not find corresponding .bai file %s. Cancelling group_bam2isoform.\n", bam_in);
+ //  Rcpp::Rcout << "Can not find corresponding .bai file " << bam_in << ". Cancelling group_bam2isoform.\n";
+ //  return;
+ // }
 
  // import all the values of fa_f
  const std::unordered_map<std::string, std::string> fa_dict = get_fa_dict(fa_file);

diff --git a/src/main-functions/match_cell_barcode.cpp b/src/main-functions/match_cell_barcode.cpp
@@ -10,7 +10,6 @@
 #include <unordered_map>
 #include <algorithm>
 #include <string>
-#include <cassert>
 #include <fstream>
 
 #include <Rcpp.h>
@@ -97,7 +96,7 @@ char complement(char n)
  case 'N':
  return 'N';
  }
- assert(false);
+ Rcpp::stop("No matching base complement");
  return ' ';
 }
 

diff --git a/src/main-functions/match_cell_barcode.h b/src/main-functions/match_cell_barcode.h
@@ -8,7 +8,6 @@
 #include <utility>
 #include <unordered_map>
 #include <string>
-#include <cassert>
 
 #include <Rcpp.h>
 

diff --git a/src/utility/json/json.h b/src/utility/json/json.h
@@ -1,3 +1,5 @@
+#include <Rcpp.h>
+
 /// Json-cpp amalgamated header (http://jsoncpp.sourceforge.net/).
 /// It is intended to be used with #include "json/json.h"
 
@@ -2296,7 +2298,7 @@ JSON_API OStream& operator<<(OStream&, const Value& root);
 #define JSON_ASSERT(condition) \
  do { \
  if (!(condition)) { \
- Json::throwLogicError("assert json failed"); \
+ Rcpp::stop("failed"); \
  } \
  } while (0)
 
@@ -2305,21 +2307,22 @@ JSON_API OStream& operator<<(OStream&, const Value& root);
  OStringStream oss; \
  oss << message; \
  Json::throwLogicError(oss.str()); \
- abort();  \
+ Rcpp::stop(oss.str()); \
  } while (0)
 
 #else // JSON_USE_EXCEPTION
 
-#define JSON_ASSERT(condition) assert(condition)
+// #define JSON_ASSERT(condition) assert(condition)
 
 // The call to assert() will show the failure message in debug builds. In
 // release builds we abort, for a core-dump or debugger.
 #define JSON_FAIL_MESSAGE(message) \
  { \
  OStringStream oss; \
  oss << message; \
- assert(false && oss.str().c_str()); \
- abort(); \
+ Rcpp::stop(oss.str().c_str());
+ //assert(false && oss.str().c_str()); 
+ //abort(); 
  }
 
 #endif