Fix readme

README.md

@@ -6,6 +6,13 @@
 
 BinSPreader is a novel tool that attempts to refine metagenome-assembled genomes (MAGs) obtained from existing tools. BinSPreader exploits the assembly graph topology and other connectivity information, such as paired-end and Hi-C reads, to refine the existing binning, correct binning errors, propagate binning from longer contigs to shorter contigs and infer contigs belonging to multiple bins.
 
+### Dependencies
+
+- g++ (version 5.3.1 or higher)
+- cmake (version 3.12 or higher)
+- zlib
+- libbz2
+
 ### Installation 
 
 ``` 
@@ -15,50 +22,89 @@ make bin-refine
 ```
 Now to run BinSPreader move to folder `assembler/` and execute 
 
-`build/bin/hicspades-binner`
+`build/bin/bin-refine`
 
 ### Input
 
-The tool has two mandatory options: 
-- 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. Alternatively, scaffolds can be provided separately using `--path` option. 
--Initial 
+The tool requires initial binning to refine, as well as assembly graph as a source of information for refining. Optionally, BinSPreader can be provided with multiple Hi-C and/or paired-end libraries.
+
+Required positional arguments: 
+
+- 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. Alternatively, scaffold paths can be provided separately using `--path` option in the `.paths` format accepted by Bandage (see [Bandage wiki](https://github.com/rrwick/Bandage/wiki/Graph-paths) for details). 
+- Binning output from an existing tool (in `.tsv` format)
+
+Synopsis: `bin-refine <graph (in GFA)> <binning (in .tsv)> <output directory> [OPTION...]`
+
+Main options:
 
-Synopsis: `hicspades-binner <graph (in GFA)> <dataset description (in YAML)> <output directory> [OPTION...]`
+- `--paths` provide contigs paths from file separately from GFA
+- `--dataset` Dataset in YAML format (see #yaml) describing Hi-C and paired-end reads
 
-The options are:
+- `-l` L Library index (0-based, default: 0). Only the library specified by this index will be used.
+- `-t` T # of threads to use (default: 1/2 of available threads)
+- `-e` E convergence relative tolerance threshold (default: 1e-5)
+- `-n` ITERATIONS maximum number of iterations (default: 5000)
+- `-m` allow multiple bin assignment (defalut: false)
+- `-Smax|-Smle` simple maximum or maximum likelihood binning assignment strategy (default: max likelihood)
+- `-Rcorr|-Rprop` Select propagation or correction mode (default: correction)
+- `--cami` use CAMI bioboxes binning format
+- `--zero-bin` emit zero bin for unbinned sequences
+- `--tall-multi` use tall table for multiple binning result
+- `--bin-dist` estimate pairwise bin distance (could be slow on large graphs!)
+- `-la` LA labels correction regularization parameter for labeled data (default: 0.6)
 
-`-t, --threads <int> `
- # of threads to use
+Sparse propagation options:
+- `--sparse-propagation` Gradually reduce regularization parameter from binned to unbinned edges. Recommended for sparse binnings with low assembly fraction.
+- `--no-unbinned-bin` Do not create a special bin for unbinned contigs. More agressive strategy.
+- `-ma, --metaalpha` Regularization parameter for sparse propagation procedure. Increase/decrease for more agressive/conservative refining (default: 0.6)
+- `-lt, --length-threshold` LENGTH_THRESHOLD Binning will not be propagated to edges longer than threshold
+- `-db' --distance-bound` DISTANCE_BOUND Binning will not be propagated further than bound from initially binned edges
 
-`-e, --enzymes <string> `
- Comma-separated string of restriction enzyme recognition sites
+Read splitting options:
+- `-r, --reads` Split reads according to binning. Can be used for reassembly.
+- `-b, --bin-weight` BIN_WEIGHT Reads bin weight threshold (default: 0.1).
 
-`--tmp-dir <dir name> `
- scratch directory to use
+Developer options:
+- `--bin-load` Load binary-converted reads from tmpdir
+- `--debug` produce lots of debug data
+- `--tmp-dir` TMP_DIR scratch directory to use
+- `-h, --help ` print help message
 
-`--min-ctg-len <int> `
- Minimum contig length for binning
+### BinSPreader output
 
-`--path-links-thr <int> `
- Minimum total number of links between contigs
+BinSPreader stores all output files in output directory `<output_dir> `, which is set by the user.
 
-`--edge-links-thr <int>` 
- Minimum number of links between long edges
+- `<output_dir>/binning.tsv` contains refined binning in `.tsv` format
+- `<output_dir>/bin_stats.tsv` contains various per-bin statistics
+- `<output_dir>/bin_weights.tsv` contains soft bin weights per contig
+- `<output_dir>/edge_weights.tsv` contains soft bin weights per edge
 
-`-h, --help `
- print help message
+In addition
+
+- `<output_dir>/bin_dist.tsv` contains refined bin distance matrix (if `--bin-dist` was used)
+- `<output_dir>/bin_label_1.fastq, <output_dir>/bin_label_2.fastq` read set for bin labeled by `bin_label` (if `--reads` was used)
+- `<output_dir>/pe_links.tsv` list of paired-end links between assembly graph edges with weights (if `--debug` was used)
+- `<output_dir>/graph_links.tsv` list of graph links between assembly graph edges with weights (if `--debug` was used)
 
 <a name="yaml"></a>
 **_Specifying input data with YAML data set file_**
 
-hicSPAdes-binner currently supports a single Hi-C library described in a YAML file. For example, if your Hi-C library is split into two pairs of files
+BinSPreader currently supports multiple paired-end or Hi-C libraries described in a YAML file. For example, if you have one paired-end library split into two sets of files
 
 ``` bash
 
- lib_hic_left_1.fastq
- lib_hic_right_1.fastq
- lib_hic_left_2.fastq
- lib_hic_right_2.fastq
+ lib_pe1_left_1.fastq
+ lib_pe1_right_1.fastq
+ lib_pe1_left_2.fastq
+ lib_pe1_right_2.fastq
+```
+
+and one Hi-C library
+
+``` bash
+
+ lib_hic1_left.fastq
+ lib_hic1_right.fastq
 ```
 
 YAML file should look like this:
@@ -68,24 +114,25 @@ YAML file should look like this:
  [
  {
  orientation: "fr",
- type: "hic",
+ type: "paired-end",
+ right reads: [
+ "/FULL_PATH_TO_DATASET/lib_pe1_right_1.fastq",
+ "/FULL_PATH_TO_DATASET/lib_pe1_right_2.fastq" 
+ ],
+ left reads: [
+ "/FULL_PATH_TO_DATASET/lib_pe1_left_1.fastq",
+ "/FULL_PATH_TO_DATASET/lib_pe1_left_2.fastq" 
+ ]
+ },
+ {
+ orientation: "fr",
+ type: "paired-end",
  right reads: [
- "/FULL_PATH_TO_DATASET/lib_hic_right_1.fastq",
- "/FULL_PATH_TO_DATASET/lib_hic_right_2.fastq" 
+ "/FULL_PATH_TO_DATASET/lib_hic1_right.fastq" 
  ],
  left reads: [
- "/FULL_PATH_TO_DATASET/lib_hic_left_1.fastq",
- "/FULL_PATH_TO_DATASET/lib_hic_left_2.fastq" 
+ "/FULL_PATH_TO_DATASET/lib_hic1_left.fastq"
  ]
  }
  ]
 ```
-
-### Output
-
-hicSPAdes-binner stores all output files in `<output_dir> `, which is set by the user.
-
-- `<output_dir>/clustering.mcl` contains resulting scaffold clustering in MCL format
-- `<output_dir>/clustering.tsv` contains resulting scaffold clustering in TSV format
-- `<output_dir>/basic_stats.tsv` contains various per-cluster statistics
-- `<output_dir>/contact_map.tsv` contains hicSPAdes scores between input scaffolds, as well as other scaffold statistics