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Better behavior with splits
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@Chris7
Chris7 committed Aug 7, 2024
1 parent c4b10ff commit 61feca4
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Showing 2 changed files with 91 additions and 59 deletions.
148 changes: 90 additions & 58 deletions src/models.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -413,17 +413,11 @@ impl BlockGroup {
let mut path_end = 0;
let mut new_edges = vec![];
let mut previous_block: Option<&Block> = None;
let mut loose_connection = false;
for block_id in &path.blocks {
let block = blocks.get(block_id).unwrap();
let block_length = (block.end - block.start);
path_end += block_length;

if loose_connection && path_start == end {
new_edges.push((Some(new_block_id), Some(block.id)));
loose_connection = false;
}

let (contains_start, contains_end, overlap) =
get_overlap(path_start, path_end, start, end);
println!(
Expand All @@ -434,78 +428,62 @@ impl BlockGroup {
// our range is fully contained w/in the block
// |----block------|
// |----range---|
let (left_block, right_block) = Block::split(
conn,
block,
block.start + start - path_start,
chromosome_index,
phased,
)
.unwrap();
Block::delete(conn, block.id);
// let left_block = Block::create(
// conn,
// &block.sequence_hash,
// block_group_id,
// block.start,
// start - path_start,
// &block.strand,
// );
// let right_block = Block::create(
// conn,
// &block.sequence_hash,
// block_group_id,
// block.start + (end - path_start),
// block.end,
// &block.strand,
// );
// if let Some(value) = previous_block {
// new_edges.push((Some(value.id), Some(left_block.id)))
// }
new_edges.push((Some(left_block.id), Some(new_block_id)));
new_edges.push((Some(new_block_id), Some(right_block.id)));
let start_split_point = block.start + start - path_start;
let end_split_point = block.start + end - path_start;
let mut next_block;
if start_split_point == block.start {
if let Some(pb) = previous_block {
new_edges.push((Some(pb.id), Some(new_block_id)));
}
next_block = block.clone();
} else {
let (left_block, right_block) =
Block::split(conn, block, start_split_point, chromosome_index, phased)
.unwrap();
Block::delete(conn, block.id);
new_edges.push((Some(left_block.id), Some(new_block_id)));
next_block = right_block.clone();
}

if end_split_point == next_block.start {
new_edges.push((Some(new_block_id), Some(next_block.id)));
} else {
let (left_block, right_block) =
Block::split(conn, &next_block, end_split_point, chromosome_index, phased)
.unwrap();
Block::delete(conn, next_block.id);
new_edges.push((Some(new_block_id), Some(left_block.id)));
}
} else if contains_start {
// our range is overlapping the end of the block
// |----block---|
// |----range---|
let split_point = block.start + start - path_start;
println!("{block:?} {split_point}");
if split_point == block.start {
// the split happens before this block begins, so it's an insert operation
if let Some(pb) = previous_block {
new_edges.push((Some(pb.id), Some(new_block_id)));
}
// we actually are skipping this block
if path_end >= end {
loose_connection = true;
}
} else {
let (left_block, right_block) =
Block::split(conn, block, split_point, chromosome_index, phased).unwrap();
Block::delete(conn, block.id);
new_edges.push((Some(left_block.id), Some(new_block_id)));
}
// let left_block = Block::create(
// conn,
// &block.sequence_hash,
// block_group_id,
// block.start,
// start - path_start,
// &block.strand,
// );
// if let Some(value) = previous_block {
// new_edges.push((Some(value.id), Some(left_block.id)));
// } else {
// new_edges.push((None, Some(left_block.id)));
// }
} else if contains_end {
// our range is overlapping the beginning of the block
// |----block---|
// |----range---|
let split_point = block.start + end - path_start;
let (left_block, right_block) =
Block::split(conn, block, split_point, chromosome_index, phased).unwrap();
Block::delete(conn, block.id);
new_edges.push((Some(new_block_id), Some(right_block.id)));
if split_point == block.start {
// the previous change ends right before this block starts, so it's an insert
new_edges.push((Some(new_block_id), Some(block.id)));
} else {
let (left_block, right_block) =
Block::split(conn, block, split_point, chromosome_index, phased).unwrap();
Block::delete(conn, block.id);
new_edges.push((Some(new_block_id), Some(right_block.id)));
}
break;
} else if overlap {
// our range is the whole block, ignore it
Expand All @@ -519,6 +497,10 @@ impl BlockGroup {
if path_start > end {
break;
}
// TODO: will we ever have a scenario where previous_block should not be set?
// for example, if overlap is true, we shouldn't be making the previous block
// an intermediary. Tests make this appear to not be a problem, but worth
// exploring fully.
previous_block = Some(block);
}

Expand Down Expand Up @@ -715,6 +697,31 @@ mod tests {
);
}

#[test]
fn insert_on_block_boundary_middle() {
let mut conn = get_connection();
let (block_group_id, path_id) = setup_block_group(&conn);
let insert_sequence = Sequence::create(&conn, "DNA", "NNNN", true);
let insert = Block::create(
&conn,
&insert_sequence,
block_group_id,
0,
4,
&"1".to_string(),
);
BlockGroup::insert_change(&mut conn, path_id, 15, 15, &insert, 1, 0);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
assert_eq!(
all_sequences,
HashSet::from_iter(vec![
"AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
"AAAAAAAAAATTTTTNNNNTTTTTCCCCCCCCCCGGGGGGGGGG".to_string()
])
);
}

#[test]
fn insert_on_block_boundary_start() {
let mut conn = get_connection();
Expand Down Expand Up @@ -815,6 +822,31 @@ mod tests {
);
}

#[test]
fn insert_spanning_blocks() {
let mut conn = get_connection();
let (block_group_id, path_id) = setup_block_group(&conn);
let insert_sequence = Sequence::create(&conn, "DNA", "NNNN", true);
let insert = Block::create(
&conn,
&insert_sequence,
block_group_id,
0,
4,
&"1".to_string(),
);
BlockGroup::insert_change(&mut conn, path_id, 5, 35, &insert, 1, 0);

let all_sequences = BlockGroup::get_all_sequences(&conn, block_group_id);
assert_eq!(
all_sequences,
HashSet::from_iter(vec![
"AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGG".to_string(),
"AAAAANNNNGGGGG".to_string()
])
);
}

#[test]
fn simple_deletion() {
let mut conn = get_connection();
Expand Down
2 changes: 1 addition & 1 deletion src/models/block.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ use rusqlite::{params_from_iter, types::Value, Connection};
use crate::models::edge::{Edge, UpdatedEdge};
use crate::models::path::PathBlock;

#[derive(Debug)]
#[derive(Clone, Debug)]
pub struct Block {
pub id: i32,
pub sequence_hash: String,
Expand Down

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