Update manual and cli

README.md

@@ -26,12 +26,49 @@ Now to run SpLitteR move to folder `assembler/` and execute
 
 ### Input
 
-#### Format
-
 The tool requires 
 
 - Assembly graph file in [GFA 1.0 format](https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md), with scaffolds included as path lines.
-- SLR library in YAML format. The tool supports SLR libraries produced using 10X Genomics Chromium and TELL-seq technologies. SLR library should be in FASTQ format with barcodes attached as BC:Z or BX:Z tags:
+- SLR library in YAML format. The tool supports SLR libraries produced using 10X Genomics Chromium and UST TELL-Seq technologies. Other SLR technologies, such as stLFR or LoopSeq can potentially be used as an input if converted to 10X or TELL-Seq format. 
+
+SpLitteR supports [LJA](https://github.com/AntonBankevich/LJA) and [Flye](https://github.com/fenderglass/Flye) assembly graphs out of the box. Other assembly graphs should prefferably be converted into blunt format by e.g. [GetBlunted](https://github.com/vgteam/GetBlunted) utility. 
+
+#### UST TELLSeq format
+
+TELL-Seq library should include barcodes, left reads, and right reads as three separate FASTQ files. 
+
+For example, if you have a TELL-Seq library
+
+``` bash
+ tellseq_reads_I1.fastq.gz
+ tellseq_reads_R1.fastq.gz
+ tellseq_reads_R2.fastq.gz
+```
+
+YAML file should look like this:
+
+``` bash
+
+ [
+ {
+ orientation: "fr",
+ type: "tell-seq",
+ right reads: [
+ "/FULL_PATH_TO_DATASET/tellseq_reads_R2.fastq.gz"
+ ],
+ left reads: [
+ "/FULL_PATH_TO_DATASET/tellseq_reads_R1.fastq.gz"
+ ],
+ aux: [
+ "/FULL_PATH_TO_DATASET/tellseq_reads_I1.fastq.gz"
+ ]
+ }
+ ]
+```
+
+#### 10X Genomics Chromium format
+
+10X library should be in FASTQ format with barcodes attached as BC:Z or BX:Z tags:
 
 ``` 
 @COOPER:77:HCYNTBBXX:1:1216:22343:0 BX:Z:AAAAAAAAAACATAGT
@@ -74,8 +111,9 @@ Main options:
 
 - `-t` Number of threads to use (default: 1/2 of available threads)
 - `--mapping-k` k-mer length for read mapping (default: 31)
-- `-Gmdbg|-Gblunt` Assembly graph type (mDBG or blunted)
+- `-Gmdbg|-Gblunt` Assembly graph type: mDBG (LJA) or blunted (Flye)
 - `-Mdiploid|-Mmeta` Repeat resolution mode (diploid or meta)
+- `--assembly-info` Path to metaFlye assembly_info.txt file (meta mode, metaFlye graphs only)
 
 Barcode index construction:
 - `--count-threshold` Minimum number of reads for barcode index
@@ -84,19 +122,28 @@ Barcode index construction:
 - `--linkage-distance` Reads are assigned to the same fragment on long edges based on the linkage distance
 - `--min-read-threshold` Minimum number of reads for path cluster extraction
 - `--relative-score-threshold` Relative score threshold for path cluster extraction
+- `--sampling-factor` Downsample input SLR reads by this factor
 
 Repeat resolution:
 - `--score` Score threshold for link index.
 - `--tail-threshold` Barcodes are assigned to the first and last <tail_threshold> nucleotides of the edge.
+- `--scaffold-links` Use scaffold links in addition to graph links for repeat resolution
 
 Developer options:
 - `--ref` Reference path for repeat resolution evaluation
-- `--statistics` Produce additional read cloud library statistics
-- `--bin-load` Load binary-converted reads from tmpdir
-- `--debug` Produce lots of debug data
+- `--bin-load` Load read-to-graph alignment
+- `--debug` Produce lots of debug data, save read-to-graph alignment
 - `--tmp-dir` Scratch directory to use
 - `-h, --help ` Print help message
 
+Example command lines:
+
+- Assembly produced LJA from HiFi diploid human dataset, with 10X SLR library (HPC compressed)\
+ `splitter lja_output/mdbg/mdbg.hpc.gfa 10x_dataset.yaml output -Mdiploid -Gmdbg`
+- Assembly produced by metaFlye from metagenomic dataset, with TELL-Seq SLR library\
+ `splitter metaflye_output/assembly_graph.gfa tellseq_dataset.yaml output --assembly-info metaflye_output/assembly_info.txt -Mmeta -Gblunt`
+- 
+
 ### Output
 
 SpLitteR stores all output files in output directory `<output_dir> `, which is set by the user.

assembler/src/projects/splitter/main.cpp

@@ -27,13 +27,13 @@ using namespace cont_index;
 using namespace path_extend::read_cloud;
 
 enum class GraphType {
-  Blunted,
-  Multiplexed
+ Blunted,
+ Multiplexed
 };
 
 enum class ResolutionMode {
-  Diploid,
-  Meta
+ Diploid,
+ Meta
 };
 
 struct gcfg {
@@ -51,7 +51,6 @@ struct gcfg {
  ResolutionMode mode = ResolutionMode::Diploid;
  bool bin_load = false;
  bool debug = false;
- bool statistics = false;
 
  //barcode_index_construction
  size_t frame_size = 40000;
@@ -83,38 +82,37 @@ static void process_cmdline(int argc, char** argv, gcfg& cfg) {
 
  auto cli = (
  graph << value("graph (in binary or GFA)"),
- file << value("SLR library description (in YAML)"),
- output_dir << value("path to output directory"),
- (option("--dataset") & value("yaml", file)) % "dataset description (in YAML)",
- (option("-l") & integer("value", cfg.libindex)) % "library index (0-based, default: 0)",
- (option("--assembly-info") & value("assembly-info", assembly_info))
- % "Path to metaflye assembly_info.txt file (meta mode, metaFlye graphs only)",
- (option("-t") & integer("value", cfg.nthreads)) % "# of threads to use",
- (option("--mapping-k") & integer("value", cfg.mapping_k)) % "k for read mapping",
- (option("--tmp-dir") & value("tmp", tmpdir)) % "scratch directory to use",
- (option("--ref") & value("reference", refpath)) % "Reference path for repeat resolution evaluation (developer option)",
- (option("--bin-load").set(cfg.bin_load)) % "load binary-converted reads from tmpdir (developer option)",
- (option("--debug").set(cfg.debug)) % "produce lots of debug data (developer option)",
- (option("--statistics").set(cfg.statistics)) % "produce additional read cloud library statistics (developer option)",
- (option("--sampling-factor") & value("sampling-factor", cfg.sampling_factor)) % "Sampling factor for read downsampling",
- (with_prefix("-G",
- option("mdbg").set(cfg.graph_type, GraphType::Multiplexed) |
- option("blunt").set(cfg.graph_type, GraphType::Blunted)) % "assembly graph type (mDBG or blunted)"),
- (with_prefix("-M",
- option("diploid").set(cfg.mode, ResolutionMode::Diploid) |
- option("meta").set(cfg.mode, ResolutionMode::Meta)) % "repeat resolution mode (diploid or meta)"),
- (option("--frame-size") & value("frame-size", cfg.frame_size)) % "Resolution of barcode index",
- (option("--linkage-distance") & value("read-linkage-distance", cfg.read_linkage_distance)) %
- "Reads are assigned to the same fragment based on linkage distance",
- (option("--score") & value("score", cfg.graph_score_threshold)) % "Score threshold for link index",
- (option("--rel-threshold") & value("rel-threshold", cfg.rel_threshold)) % "Relative score threshold for vertex resolution",
- (option("--tail-threshold") & value("tail-threshold", cfg.tail_threshold)) %
- "Barcodes are assigned to the first and last <tail_threshold> nucleotides of the edge",
- (option("--count-threshold") & value("count-threshold", cfg.count_threshold))
- % "Minimum number of reads for barcode index",
- (option("--scaffold-links").set(cfg.scaffold_links)) % "Use scaffold links in the vertex resolution",
- (option("--length-threshold") & value("length-threshold", cfg.length_threshold))
- % "Minimum scaffold graph edge length (meta mode option)"
+ file << value("SLR library description (in YAML)"),
+ output_dir << value("path to output directory"),
+ (option("--dataset") & value("yaml", file)) % "dataset description (in YAML)",
+ (option("-l") & integer("value", cfg.libindex)) % "library index (0-based, default: 0)",
+ (option("--assembly-info") & value("assembly-info", assembly_info))
+ % "Path to metaflye assembly_info.txt file (meta mode, metaFlye graphs only)",
+ (option("-t") & integer("value", cfg.nthreads)) % "# of threads to use",
+ (option("--mapping-k") & integer("value", cfg.mapping_k)) % "k for read mapping",
+ (option("--tmp-dir") & value("tmp", tmpdir)) % "scratch directory to use",
+ (option("--ref") & value("reference", refpath)) % "Reference path for repeat resolution evaluation (developer option)",
+ (option("--bin-load").set(cfg.bin_load)) % "load binary-converted reads from tmpdir (developer option)",
+ (option("--debug").set(cfg.debug)) % "produce lots of debug data (developer option)",
+ (option("--sampling-factor") & value("sampling-factor", cfg.sampling_factor)) % "Sampling factor for read downsampling",
+ (with_prefix("-G",
+ option("mdbg").set(cfg.graph_type, GraphType::Multiplexed) |
+ option("blunt").set(cfg.graph_type, GraphType::Blunted)) % "assembly graph type (mDBG or blunted)"),
+ (with_prefix("-M",
+ option("diploid").set(cfg.mode, ResolutionMode::Diploid) |
+ option("meta").set(cfg.mode, ResolutionMode::Meta)) % "repeat resolution mode (diploid or meta)"),
+ (option("--frame-size") & value("frame-size", cfg.frame_size)) % "Resolution of barcode index",
+ (option("--linkage-distance") & value("read-linkage-distance", cfg.read_linkage_distance)) %
+ "Reads are assigned to the same fragment based on linkage distance",
+ (option("--score") & value("score", cfg.graph_score_threshold)) % "Score threshold for link index",
+ (option("--rel-threshold") & value("rel-threshold", cfg.rel_threshold)) % "Relative score threshold for vertex resolution",
+ (option("--tail-threshold") & value("tail-threshold", cfg.tail_threshold)) %
+ "Barcodes are assigned to the first and last <tail_threshold> nucleotides of the edge",
+ (option("--count-threshold") & value("count-threshold", cfg.count_threshold))
+ % "Minimum number of reads for barcode index",
+ (option("--scaffold-links").set(cfg.scaffold_links)) % "Use scaffold links in addition to graph links for repeat resolution",
+ (option("--length-threshold") & value("length-threshold", cfg.length_threshold))
+ % "Minimum scaffold graph edge length (meta mode option)"
  );
 
  auto result = parse(argc, argv, cli);
@@ -154,16 +152,16 @@ struct TimeTracerRAII {
 };
 
 gfa::GFAReader ReadGraph(const gcfg &cfg,
- debruijn_graph::Graph &graph,
- io::IdMapper<std::string> *id_mapper) {
+  debruijn_graph::Graph &graph,
+  io::IdMapper<std::string> *id_mapper) {
  switch (cfg.graph_type) {
  default:
  FATAL_ERROR("Unknown graph representation type");
  case GraphType::Multiplexed: {
  gfa::GFAReader gfa(cfg.graph);
  gfa.to_graph(graph, id_mapper);
-  INFO("GFA segments: " << gfa.num_edges() << ", links: " << gfa.num_links() << ", paths: "
-  << gfa.num_paths());
+  INFO("GFA segments: " << gfa.num_edges() << ", links: " << gfa.num_links() << ", paths: "
+ << gfa.num_paths());
  return gfa;
  }
  }
@@ -281,7 +279,7 @@ cont_index::VertexResults GetRepeatResolutionResults(const gcfg &cfg,
  case ResolutionMode::Meta: {
  auto repetitive_edges = ParseRepetitiveEdges(graph, cfg.assembly_info, id_mapper);
  auto repeat_predicate = [&repetitive_edges](const debruijn_graph::EdgeId &edge) {
-  return repetitive_edges.find(edge) == repetitive_edges.end();
+ return repetitive_edges.find(edge) == repetitive_edges.end();
  };
  contracted_graph::DBGContractedGraphFactory factory(graph, repeat_predicate);
  factory.Construct();