preliminary contigs + contig output saves

ablab · Feb 28, 2017 · ee94553 · ee94553
1 parent 50d56ea
commit ee94553
Show file tree

Hide file tree

Showing 5 changed files with 18 additions and 16 deletions.
diff --git a/assembler/src/projects/spades/contig_output_stage.cpp b/assembler/src/projects/spades/contig_output_stage.cpp
@@ -11,7 +11,7 @@
 namespace debruijn_graph {
 
 void ContigOutput::run(conj_graph_pack &gp, const char*) {
- auto output_dir = cfg::get().output_dir;
+ auto output_dir = cfg::get().output_dir + contig_name_prefix_;
 
  OutputContigs(gp.g, output_dir + "before_rr", false);
  OutputContigsToFASTG(gp.g, output_dir + "assembly_graph", gp.components);
@@ -45,7 +45,7 @@ void ContigOutput::run(conj_graph_pack &gp, const char*) {
 
  writer.OutputPaths(gp.contig_paths, output_dir + cfg::get().co.scaffolds_name);
 
- OutputContigsToGFA(gp.g, gp.contig_paths, cfg::get().output_dir + "assembly_graph");
+ OutputContigsToGFA(gp.g, gp.contig_paths, output_dir + "assembly_graph");
  } else {
  OutputContigs(gp.g, output_dir + "simplified_contigs", cfg::get().use_unipaths);
  OutputContigs(gp.g, output_dir + cfg::get().co.contigs_name, false);

diff --git a/assembler/src/projects/spades/contig_output_stage.hpp b/assembler/src/projects/spades/contig_output_stage.hpp
@@ -15,15 +15,15 @@ namespace debruijn_graph {
 class ContigOutput : public spades::AssemblyStage {
 private:
  bool output_paths_;
-public:
- ContigOutput(bool output_paths = true)
- : AssemblyStage("Contig Output", "contig_output"), output_paths_(output_paths) { }
-
- void load(conj_graph_pack &, const std::string &, const char *) { }
+ string contig_name_prefix_;
 
- void save(const conj_graph_pack &, const std::string &, const char *) const { }
+public:
+ ContigOutput(bool output_paths = true, bool preliminary = false, const string& contig_name_prefix = "")
+ : AssemblyStage("Contig Output", preliminary ? "preliminary_contig_output" : "contig_output"),
+ output_paths_(output_paths), contig_name_prefix_(contig_name_prefix) { }
 
  void run(conj_graph_pack &gp, const char *);
+
 };
 
 }
diff --git a/assembler/src/projects/spades/launch.hpp b/assembler/src/projects/spades/launch.hpp
@@ -96,12 +96,13 @@ void assemble_genome() {
  SPAdes.add(new debruijn_graph::MismatchCorrection());
  if (cfg::get().rr_enable) {
  if (two_step_rr) {
+ string prelim_prefix = "preliminary_";
  if (cfg::get().use_intermediate_contigs)
  SPAdes.add(new debruijn_graph::PairInfoCount(true))
  .add(new debruijn_graph::DistanceEstimation(true))
  .add(new debruijn_graph::RepeatResolution(true))
- .add(new debruijn_graph::ContigOutput())
- .add(new debruijn_graph::SecondPhaseSetup());
+ .add(new debruijn_graph::ContigOutput(true, true, prelim_prefix))
+ .add(new debruijn_graph::SecondPhaseSetup(prelim_prefix));
 
  SPAdes.add(new debruijn_graph::Simplification());
  }
@@ -119,12 +120,10 @@ void assemble_genome() {
 
  //No graph modification allowed after HybridLibrariesAligning stage!
 
- SPAdes.add(new debruijn_graph::ContigOutput(false))
+ SPAdes.add(new debruijn_graph::ContigOutput(false, false, "pre_pe_"))
  .add(new debruijn_graph::PairInfoCount())
  .add(new debruijn_graph::DistanceEstimation())
  .add(new debruijn_graph::RepeatResolution());
- } else {
- SPAdes.add(new debruijn_graph::ContigOutput(false));
  }
 
  SPAdes.add(new debruijn_graph::ContigOutput());

diff --git a/assembler/src/projects/spades/second_phase_setup.cpp b/assembler/src/projects/spades/second_phase_setup.cpp
@@ -21,7 +21,7 @@ void SecondPhaseSetup::run(conj_graph_pack &gp, const char*) {
  gp.ClearRRIndices();
  gp.ClearPaths();
 
- std::string old_pe_contigs_filename = cfg::get().output_dir + "final_contigs.fasta";
+ std::string old_pe_contigs_filename = cfg::get().output_dir + contig_name_prefix_ + "final_contigs.fasta";
  std::string new_pe_contigs_filename = cfg::get().output_dir + "first_pe_contigs.fasta";
 
  VERIFY(path::check_existence(old_pe_contigs_filename));

diff --git a/assembler/src/projects/spades/second_phase_setup.hpp b/assembler/src/projects/spades/second_phase_setup.hpp
@@ -12,9 +12,12 @@ namespace debruijn_graph {
 
 //todo rename
 class SecondPhaseSetup : public spades::AssemblyStage {
+private:
+ string contig_name_prefix_;
+
 public:
- SecondPhaseSetup()
- : AssemblyStage("Second Phase Setup", "second_phase_setup") { }
+ SecondPhaseSetup(const string& contig_name_prefix = "")
+ : AssemblyStage("Second Phase Setup", "second_phase_setup"),contig_name_prefix_(contig_name_prefix)  { }
 
  void run(conj_graph_pack &gp, const char *);
 };