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WIP: solidify start #63

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WIP: solidify start #63

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0284022
initial go at #59
brentp Sep 12, 2022
fb42dac
bed format to region format requires adding 1 to start.
brentp Sep 23, 2022
93031ff
remove extra logic from ssio/reader
brentp Nov 16, 2022
a731879
revert launch.json change
brentp Nov 16, 2022
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9 changes: 6 additions & 3 deletions d4tools/src/show/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,11 @@ fn parse_region_spec<T: Iterator<Item = String>>(
for region_spec in regions {
if let Some(captures) = region_pattern.captures(&region_spec) {
let chr = captures.name("CHR").unwrap().as_str();
let start: u32 = captures
// since we are reading a region like chr:start-end which is 1-based, we subtract 1 from the start.
let start: u32 = std::cmp::max(1, captures
.name("FROM")
.map_or(0u32, |x| x.as_str().parse().unwrap_or(0));
.map_or(0u32, |x| x.as_str().parse().unwrap_or(0))) - 1;

let end: u32 = captures
.name("TO")
.map_or_else(|| {
Expand Down Expand Up @@ -311,7 +313,8 @@ pub fn entry_point(args: Vec<String>) -> Result<(), Box<dyn std::error::Error>>
if raw_chr.is_some() && raw_beg.is_some() && raw_end.is_some() {
if let Ok(begin) = raw_beg.unwrap().parse::<u32>() {
if let Ok(end) = raw_end.unwrap().parse::<u32>() {
region_list.push(format!("{}:{}-{}", raw_chr.unwrap(), begin, end));
// region-file is bed format so we add 1 to start to get to chr:start-end
region_list.push(format!("{}:{}-{}", raw_chr.unwrap(), begin + 1, end));
}
}
buf.clear();
Expand Down