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Fix edge case where the ts inner is at the boundaries of the sequences. #182

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Merged
sebschmi merged 1 commit into from
May 13, 2026
Merged

Fix edge case where the ts inner is at the boundaries of the sequences. #182

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20 changes: 12 additions & 8 deletions lib_tsshow/src/ts_arrangement/inner.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -330,15 +330,19 @@ impl TsInnerArrangement {
.iter()
.take_while(|(_, c)| c.is_blank())
.last()
.unwrap()
.0;
.map(|(i, _)| i);
let first_final_blank = inner
.iter()
.rev()
.take_while(|(_, c)| c.is_blank())
.last()
.unwrap()
.0;
.map(|(i, _)| i)
.unwrap_or(inner.len().into());
Comment thread
sebschmi marked this conversation as resolved.
let first_non_blank = inner
.iter()
.find(|(_, c)| !c.is_blank())
.map(|(i, _)| i)
.unwrap();
let first_source_column = inner
.iter_values()
.filter(|c| c.is_source_char())
Expand All @@ -355,7 +359,8 @@ impl TsInnerArrangement {
assert!(first_source_column >= last_source_column);

// Add prefix to extend to max_end.
let mut arrangement_column = last_initial_blank + 1usize;
let mut arrangement_column =
last_initial_blank.map(|i| i + 1usize).unwrap_or(0.into());
let mut source_column = first_source_column;
#[allow(clippy::explicit_counter_loop)]
for _ in 0..ts.equal_cost_range.max_end {
Expand Down Expand Up @@ -384,15 +389,14 @@ impl TsInnerArrangement {
}

// Convert prefix to extend to min_end.
let mut arrangement_column = last_initial_blank;
let mut arrangement_column = first_non_blank;
for _ in 0..-ts.equal_cost_range.min_end {
arrangement_column += 1;

while !inner[arrangement_column].is_source_char() {
arrangement_column += 1;
}

inner[arrangement_column].to_optional();
arrangement_column += 1;
}

// Convert suffix to extend to max_start.
Expand Down
4 changes: 4 additions & 0 deletions test_files/LINC01349_20.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
>Homo_sapiens
ACTGAAAAAGAGCTTCAGTATCTTATGGAGCCTCAAGAAGCCAAAGCTTTTAGAAGTCCCAGCCCCTAAGGCTTGATGGGGGTGGATGGAAGTCATCAAGGGAGATCTGTCTAACAGCTATTTAGAGTGTACTCTTGATTGCTGTTTCCTGAAAAAGGAGTCTTGTACCAGCTACTTGCGGAAATTAGTGGGTAAATTTTCTAGTCAGCATTATTTATAAGCTTCTGGAGAATTTATGAACATTAATATGATGTTGGGAAAAAAGCTGTGAATGTTATAATGTAAAATTGGGGTGGGGAGGGGTCCAGGATGGCTGAGTAGAAGCAGCTGTGGTGTGTGGCTCTCAAGGAGAGGAATGAAAGGGCCAAGTGAATACAGCACCTTCTATTGAAATATCCAGGTTCTCGCATTGGTACTGATGAGGAAAACAACTCA
>PrimatesAnc069
ACTGAAAAAGAGCTTCAGTGTCTTATGGAGCCTCAAGAAGCCAAAGCTTTTAGAAGTCCCAGCCCCTAAGGCTTGATGGGGGTGGATGGAAGTCATCAAGGGAGATCTGTCTAACAGCTATTTAGAGTGTACTCTTGATTGCTGTTTCCTGAAAAAGGAGTCTTGTACCAGCTACTTGCGGAAATTAGTGGGTAAATTT------------------------------------ATGAACATTAATATGATGTTGGGAAAAAAGCTGTGAATGTTATAATGTAAAATTGGGGTGGGGAGGGGTCCAGGATGGCTGAGTAGAAGCAGCTGTGGTGTGTGGCTCTCAAGGAGAGGAATGAAAGGGCCAAGTGAATACAGCACCTTCTATTGAAATATCCAGGTTCTCGCATTGGTACTGATGAGGAAAACAACTCA
3 changes: 3 additions & 0 deletions test_files/LINC01349_20.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
#!/usr/bin/env bash

Comment thread
sebschmi marked this conversation as resolved.
cargo run -- show -i test_files/LINC01349_20.toml -n test_files/LINC01349_20.no_ts.toml -s test_files/LINC01349_20.svg -pare -z5
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