Merge branch 'dev-c++11' of http:https://github.com/chungongyu/siga into de…

…v-c++11
chungongyu · Nov 9, 2020 · f95c315 · f95c315
2 parents a162ab0 + 766dec1
commit f95c315
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Showing 3 changed files with 39 additions and 4 deletions.
diff --git a/src/assembler.cpp b/src/assembler.cpp
@@ -92,7 +92,7 @@ class Assembler : public Runner {
  // Trimming
  size_t trimRound = 0, numTrimRounds = options.get<size_t>("cut-terminal", 10);
  while (trimRound < numTrimRounds) {
- LOG4CXX_INFO(logger, boost::format("[Trim] Trim round: %d") % (trimRound + 1))
+ LOG4CXX_INFO(logger, boost::format("[Trim] Trim round: %d") % (trimRound + 1));
  bool modified = false;
 
  LOG4CXX_INFO(logger, "Trimming tips");
@@ -118,7 +118,7 @@ class Assembler : public Runner {
  // Trimming
  size_t trimRound = 0, numTrimRounds = options.get<size_t>("cut-terminal", 10);
  while (trimRound < numTrimRounds) {
- LOG4CXX_INFO(logger, boost::format("[Trim] Trim round: %d") % (trimRound + 1))
+ LOG4CXX_INFO(logger, boost::format("[Trim] Trim round: %d") % (trimRound + 1));
  bool modified = false;
 
  LOG4CXX_INFO(logger, "Removing loops");

diff --git a/src/bigraph.cpp b/src/bigraph.cpp
@@ -66,8 +66,8 @@ void Edge::validate() const {
  LOG4CXX_ERROR(logger, "Error, matching strings are not the same length");
  LOG4CXX_ERROR(logger, boost::format("V1M: %s,%s") % start()->id() % m1);
  LOG4CXX_ERROR(logger, boost::format("V2M: %s,%s") % end()->id() % m2);
- LOG4CXX_ERROR(logger, boost::format("V1: %s") % v1)
- LOG4CXX_ERROR(logger, boost::format("V2: %s") % v2)
+ LOG4CXX_ERROR(logger, boost::format("V1: %s") % v1);
+ LOG4CXX_ERROR(logger, boost::format("V2: %s") % v2);
  assert(false);
  }
 }

diff --git a/test/index_test.cpp b/test/index_test.cpp
@@ -45,4 +45,39 @@ BOOST_AUTO_TEST_CASE(RLUnit_test) {
  }
 }
 
+BOOST_AUTO_TEST_CASE(RLString_test) {
+ DNASeq read("test", "AAACGGGTA");
+
+ RLString runs;
+
+ RLUnit run;
+ for (const auto& c : read.seq) {
+ if (run.initialized()) {
+ if (run == c && !run.full()) {
+ ++run;
+ } else {
+ runs.push_back(run);
+ run = RLUnit(c);
+ }
+ } else {
+ run = RLUnit(c);
+ }
+ }
+ if (run.initialized()) {
+ runs.push_back(run);
+ }
+
+ BOOST_CHECK_EQUAL(runs.size(), 5);
+ BOOST_CHECK_EQUAL(runs[0], 'A');
+ BOOST_CHECK_EQUAL(runs[0].count(), 3);
+ BOOST_CHECK_EQUAL(runs[1], 'C');
+ BOOST_CHECK_EQUAL(runs[1].count(), 1);
+ BOOST_CHECK_EQUAL(runs[2], 'G');
+ BOOST_CHECK_EQUAL(runs[2].count(), 3);
+ BOOST_CHECK_EQUAL(runs[3], 'T');
+ BOOST_CHECK_EQUAL(runs[3].count(), 1);
+ BOOST_CHECK_EQUAL(runs[4], 'A');
+ BOOST_CHECK_EQUAL(runs[4].count(), 1);
+}
+
 BOOST_AUTO_TEST_SUITE_END();