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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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7 changes: 4 additions & 3 deletions .vscode/launch.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
"version": "0.2.0",
"configurations": [

{
"type": "lldb",
"request": "launch",
Expand All @@ -15,9 +16,9 @@
]
},
"program": "target/debug/d4tools",
"env": {"RUST_LOG": "info"},
"args": ["create", "-g", "/tmp/1.g", "/tmp/1.bedgraph"],
"cwd": "/tmp"
"env": {"RUST_LOG": "info", "RUST_BACKTRACE": "1"},
"args": ["view", "${workspaceFolder}/fdr.peaks.d4", "chr1:1-59999"],
"cwd": "${workspaceFolder}"
},
{
"type": "lldb",
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6 changes: 5 additions & 1 deletion d4/src/ssio/reader.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -131,8 +131,10 @@ impl<R: Read + Seek> D4TrackReader<R> {
if table_ref.chrom_id == chrom_id {
let overlap_begin = table_ref.begin.max(begin);
let overlap_end = table_ref.end.min(end);

if overlap_begin < overlap_end {
if overlap_begin == table_ref.begin || self.sfi.is_none() {
//if overlap_begin + 1 == table_ref.begin || self.sfi.is_none() {
if self.sfi.is_none() {
secondary_view.push(table_ref.clone());
} else {
let sfi = self.sfi.as_ref().unwrap();
Expand All @@ -147,6 +149,8 @@ impl<R: Read + Seek> D4TrackReader<R> {
));
}
}
} else {
break;
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@38 38 Nov 18, 2022

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I think this introduce new bug. Basically this is the part that creates a view to secondary table partitions that contains the data points that is related to the query.

If break at this point, I believe this will introduce bug in some query for large interval which is larger than a secondary table partition.

So I am a little bit confused if the issue is just change the interval convention, what is the problem that needs to be fixed at this point.

To help me understand the change better, could you please give me some data that triggers a buggy output.

Thanks,
Hao

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@mrvollger mrvollger Nov 18, 2022 •
edited
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Hi @38, in case it helps I link to data that appears to be bugged in issue #59 and walk through the example.

Edit: never mind I see this is unrelated to 59 which you have fixed. Thanks!

}
}
}
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9 changes: 6 additions & 3 deletions d4tools/src/show/main.rs
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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