PredictHaplo

This repository is used for the continued development of PredictHaplo. See the publication for more information:

• Prabhakaran, S., Rey, M., Zagordi, O., Beerenwinkel, N., & Roth, V. (2013). HIV haplotype inference using a propagating dirichlet process mixture model. IEEE/ACM transactions on computational biology and bioinformatics, 11(1), 182-191.

We adapt the SCYTHE library from MCMCpack's implementation.

Compilation

$ cmake -DCMAKE_BUILD_TYPE=Release -B build -S .
$ cmake --build build

Usage

$ predicthaplo --help
Usage: predicthaplo [OPTIONS]

  This software aims at reconstructing haplotypes from next-generation sequencing data.

Options:
  --sam FILE                        Filename of the aligned reads (sam format).
  --reference FILE                  Filename of reference sequence (FASTA).
  --prefix STR                      Prefix of output files.
  --visualization_level INT         do_visualize (1 = true, 0 = false).
  --have_true_haplotypes INT        have_true_haplotypes (1 = true, 0 = false).
  --true_haplotypes FILE            Filename of the true haplotypes (MSA in FASTA format) (fill in any dummy filename if there is no "true" haplotypes).
  --do_local_Analysis INT           do_local_analysis (1 = true, 0 = false) (must be 1 in the first run).
  --max_reads_in_window INT         ...
  --entropy_threshold FLOAT         ...
  --reconstruction_start INT        ...
  --reconstruction_stop INT         ...
  --min_mapping_qual INT            ...
  --min_readlength INT              ...
  --max_gap_fraction FLOAT          Relative to alignment length.
  --min_align_score_fraction FLOAT  Relative to read length.
  --alpha_MN_local FLOAT            Prior parameter for multinomial tables over the nucleotides.
  --min_overlap_factor FLOAT        Reads must have an overlap with the local reconstruction window of at least this factor times the window size.
  --local_window_size_factor FLOAT  Size of  local reconstruction window relative to the median of the read lengths.
  --cluster_number INT              Max number of clusters (in the truncated Dirichlet process).
  --nSample INT                     MCMC iterations.
  --include_deletions INT           Include deletions (0 = no, 1 = yes).
  --help                            Show this message and exit.

Tests

This project comes with unit tests that are disabled by default. To enable these tests use the following flag when generating the build system: -DPHAPLO_ENABLE_UNIT_TESTS:BOOL=ON. Note that the googletest library is required and linked in this case.