twitcher 0.6.5

Find template switch mutations in genomic data
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34

pub const VCF_HEADER_TWITCHER_VERSION_KEY: &str = "twitcher_version";
pub const TWITCHER_VERSION: &str = env!("CARGO_PKG_VERSION");
pub const VCF_HEADER_TWITCHER_CMD: &str = "twitcher_cmd";

pub const VCF_TS_CIGARETS_KEY: &str = "CIGARETS";
pub const VCF_TS_CIGARETS_DESC: &str =
    "CIGARETS string for this alignment, which can include one or more template switches";

pub const VCF_TS_COST_KEY: &str = "TSCOST";
pub const VCF_TS_COST_DESC: &str =
    "Alignment cost of the template switch realignment for this cluster";

pub const VCF_TS_INNER_LEN_KEY: &str = "TSINNERLEN";
pub const VCF_TS_INNER_LEN_DESC: &str =
    "Inner length of each template switch in this record (number of ancestor aligned bases)";

pub const VCF_TS_JUMP_KEY: &str = "TSJUMP";
pub const VCF_TS_JUMP_DESC: &str =
    "Jump distance from switchpoint 1 to switchpoint 2 for each template switch in this record";

pub const VCF_TS_ID_KEY: &str = "TSID";
pub const VCF_TS_ID_DESC: &str = "Cluster identifier shared by all records from the same realignment; matches the id column in CSV output";

pub const VCF_CLUSTER_GRP_KEY: &str = "CLUSTERGRP";
pub const VCF_CLUSTER_GRP_DESC: &str = "Proximity cluster group identifier, shared by all haplotype sub-clusters originating from the same proximity cluster";

pub const VCF_TWITCHER_PHASE_KEY: &str = "TWITCHERPHASE";
pub const VCF_TWITCHER_PHASE_DESC: &str = "Present when the genotype (GT) and/or phase set (PS) of this record differs from the input VCF, i.e. was assigned by this program rather than inherited";

/// FORMAT fields this program writes itself, so they must be declared even when the input
/// header does not declare them. See `vcf::ensure_written_format_fields`.
pub const VCF_FORMAT_GT_LINE: &[u8] =
    b"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">";
pub const VCF_FORMAT_PS_LINE: &[u8] = b"##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase set identifier shared by all records in a haplotype sub-cluster\">";