Install requirements: rust ver 1.3 or later, clang
curl https://sh.rustup.rs -sSf | sh
echo 'export PATH=~/.cargo/bin:$PATH' >> ~/.bashrc
source ~/.bashrc
which cargo
If the build fails on the htslib dependency you might need xz.
export CFLAGS='-I/path/to/xz/<version>/include'
or add that to your .bashrc and source it
Then you should be able to clone and install the project.
git clone https://github.com/wheaton5/haplovalidate
cd haplovalidate
cargo build --release
And the usage is.
./target/release/haplo_validate -h
het_snp_kmers 1.0
Haynes Heaton <[email protected]>
Finds kmer pairs that are different in the middle base and each have roughly haploid coverage. Meant for illumina data
as an initial step for de novo phasing.
USAGE:
haplo_validate [OPTIONS] --primary_fasta <primary_fasta> --secondary_fasta <secondary_fasta>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-k, --het_kmers <het_kmers> file containing het kmer pairs as output by het_kmer_pair tool <kmer1>
<count> <kmer2> <count> per file
-i, --primary_fasta <primary_fasta> primary assembly fasta
-s, --secondary_fasta <secondary_fasta> alt fasta representing contigs from the second haplotype
which will tell you how many kmer pairs are in each assembly in a number of configurations such as seeing one is the primary and the other in the secondary (true phased)