notes.md

Notes For Developer

Current workflow

Now we expect to work in the following way:

• extract to extract information from BAM or PAIRS files. (Input: .fasta, .bam/.pairs, Output: .hmr_nodes, .hmr_reads)
• draft to generate graph information. (Input: .hmr_nodes and .hmr_reads, Output: nodes .hmr_nodes and edges .hmr_edges)
• partition to generate group nodes. (Input: .hmr_nodes and .hmr_edges, Output: node group files .hmr_group)
• ordering to sort the nodes. (Input: .hmr_nodes, .hmr_edges and .hmr_group, Output: node sequence files .hmr_seq)
• orientation to decide the orientation of the node groups. (Input: .hmr_nodes, .hmr_reads and .hmr_seq, Output: chromosome sequence files .hmr_chromo)
• build to generate results. (Input: .hmr_nodes, .fasta, .hmr_chromo, Output: .fasta)

Allele checklist:

• Apply allele constraints partition.
• Apply allele table filtering
• Apply non-best filtering

Feature support:

• Automated pipeline
• Pairs format support
• Chromap support