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Merged
sebschmi merged 1 commit into from
May 7, 2026
Merged

Separate costs for inter and intra TS #165

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9 changes: 6 additions & 3 deletions lib_ts_chainalign/src/chaining_lower_bounds/ts_jump/tests.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@ fn test_max_match_run_0() {
},
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..200,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -65,7 +66,8 @@ fn test_max_match_run_1() {
},
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..200,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -110,7 +112,8 @@ fn test_max_match_run_2() {
},
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..200,
ancestor_gap: -100..100,
Expand Down
10 changes: 7 additions & 3 deletions lib_ts_chainalign/src/costs.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,12 @@ pub struct GapAffineCosts<Cost> {

#[derive(Debug, Clone, Serialize, Deserialize, Eq, PartialEq)]
pub struct TsLimits {
/// The maximum range of the 12-jump of a template switch.
/// The maximum range of the 12-jump of an inter (12 or 21) template switch.
/// This parameter is ignored for now.
pub jump_12: Range<isize>,
pub inter_jump_12: Range<isize>,
/// The maximum range of the 12-jump of an intra (11 or 22) template switch.
/// This parameter is ignored for now.
pub intra_jump_12: Range<isize>,
/// The maximum range of the 34-jump of a template switch.
Comment thread
sebschmi marked this conversation as resolved.
/// This parameter is ignored for now.
pub jump_34: Range<isize>,
Expand Down Expand Up @@ -63,7 +66,8 @@ impl<Cost: Zero> GapAffineCosts<Cost> {
impl TsLimits {
pub fn new_unlimited() -> Self {
Self {
jump_12: isize::MIN..isize::MAX,
inter_jump_12: isize::MIN..isize::MAX,
intra_jump_12: isize::MIN..isize::MAX,
jump_34: isize::MIN..isize::MAX,
length_23: usize::MIN..usize::MAX,
ancestor_gap: isize::MIN..isize::MAX,
Expand Down
3 changes: 2 additions & 1 deletion lib_ts_chainalign/src/costs/compat.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ impl<AlphabetType: Alphabet, Cost: AStarCost> From<TemplateSwitchConfig<Alphabet
.into(),
ts_base_cost,
ts_limits: TsLimits {
jump_12: value.offset_costs.zero_range().unwrap(),
inter_jump_12: value.rq_qr_offset_costs.zero_range().unwrap(),
intra_jump_12: value.rr_qq_offset_costs.zero_range().unwrap(),
// tsalign costs do not support limiting this.
jump_34: isize::MIN..isize::MAX,
length_23: value.length_costs.zero_range().unwrap(),
Expand Down
27 changes: 18 additions & 9 deletions lib_ts_chainalign/src/exact_chaining/ts_12_jump/tests.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,8 @@ fn test_start_end() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -86,7 +87,8 @@ fn test_partial_alignment() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -134,7 +136,8 @@ fn test_gap_directions() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -189,7 +192,8 @@ fn test_max_match_run_0() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -235,7 +239,8 @@ fn test_max_match_run_1() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -283,7 +288,8 @@ fn test_max_match_run_2() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -338,7 +344,8 @@ fn test_only_jump() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -381,7 +388,8 @@ fn test_only_jump_start() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -424,7 +432,8 @@ fn test_only_jump_end() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down
27 changes: 18 additions & 9 deletions lib_ts_chainalign/src/exact_chaining/ts_34_jump/tests.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,8 @@ fn test_start_end() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -80,7 +81,8 @@ fn test_partial_alignment() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -122,7 +124,8 @@ fn test_gap_directions() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -171,7 +174,8 @@ fn test_max_match_run_0() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -211,7 +215,8 @@ fn test_max_match_run_1() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -259,7 +264,8 @@ fn test_max_match_run_2() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -308,7 +314,8 @@ fn test_only_jump() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -345,7 +352,8 @@ fn test_only_jump_start() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down Expand Up @@ -382,7 +390,8 @@ fn test_only_jump_end() {
),
ts_base_cost: U32Cost::from(2u8),
ts_limits: TsLimits {
jump_12: -100..100,
inter_jump_12: -100..100,
intra_jump_12: -100..100,
jump_34: -100..100,
length_23: 0..100,
ancestor_gap: -100..100,
Expand Down
36 changes: 22 additions & 14 deletions lib_tsalign/src/a_star_aligner/alignment_result/alignment/template_switch_specifics.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -744,9 +744,11 @@ impl Alignment<AlignmentType> {
secondary = ts_secondary;
direction = ts_direction;
let cost_increment = config.base_cost.get(primary, secondary, direction);
let Some(cost_increment) =
cost_increment.checked_add(&config.offset_costs.evaluate(&first_offset))
else {
let Some(cost_increment) = cost_increment.checked_add(
&config
.offset_costs(primary, secondary)
.evaluate(&first_offset),
) else {
return Cost::max_value();
};
primary_index = match primary {
Expand Down Expand Up @@ -863,22 +865,22 @@ mod tests {
static START_COSTS: LazyLock<Vec<U64Cost>> = LazyLock::new(|| {
[
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&-6)
+ CONFIG.rq_qr_offset_costs.evaluate(&-6)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&2)
+ CONFIG.length_costs.evaluate(&2)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&-4)
+ CONFIG.rq_qr_offset_costs.evaluate(&-4)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&3)
+ CONFIG.length_costs.evaluate(&3)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&-2)
+ CONFIG.rq_qr_offset_costs.evaluate(&-2)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&4)
+ CONFIG.length_costs.evaluate(&4)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&0)
+ CONFIG.rq_qr_offset_costs.evaluate(&0)
+ CONFIG.secondary_reverse_edit_costs.substitution_cost(
DnaAlphabet::ascii_to_character(b'G').unwrap(),
DnaAlphabet::ascii_to_character(b'T').unwrap(),
Expand All @@ -887,7 +889,7 @@ mod tests {
+ CONFIG.length_costs.evaluate(&5)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&2)
+ CONFIG.rq_qr_offset_costs.evaluate(&2)
+ CONFIG.secondary_reverse_edit_costs.substitution_cost(
DnaAlphabet::ascii_to_character(b'G').unwrap(),
DnaAlphabet::ascii_to_character(b'T').unwrap(),
Expand Down Expand Up @@ -1017,22 +1019,22 @@ mod tests {
static END_COSTS: LazyLock<Vec<U64Cost>> = LazyLock::new(|| {
[
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&10)
+ CONFIG.rq_qr_offset_costs.evaluate(&10)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&2)
+ CONFIG.length_costs.evaluate(&2)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&10)
+ CONFIG.rq_qr_offset_costs.evaluate(&10)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&3)
+ CONFIG.length_costs.evaluate(&3)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&10)
+ CONFIG.rq_qr_offset_costs.evaluate(&10)
+ CONFIG.reverse_anti_primary_gap_costs.evaluate(&4)
+ CONFIG.length_costs.evaluate(&4)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&10)
+ CONFIG.rq_qr_offset_costs.evaluate(&10)
+ CONFIG.secondary_reverse_edit_costs.substitution_cost(
DnaAlphabet::ascii_to_character(b'A').unwrap(),
DnaAlphabet::ascii_to_character(b'C').unwrap(),
Expand All @@ -1041,7 +1043,7 @@ mod tests {
+ CONFIG.length_costs.evaluate(&5)
+ CONFIG.length_difference_costs.evaluate(&0),
CONFIG.base_cost.rqr
+ CONFIG.offset_costs.evaluate(&10)
+ CONFIG.rq_qr_offset_costs.evaluate(&10)
+ CONFIG.secondary_reverse_edit_costs.substitution_cost(
DnaAlphabet::ascii_to_character(b'A').unwrap(),
DnaAlphabet::ascii_to_character(b'C').unwrap(),
Expand Down Expand Up @@ -1207,7 +1209,13 @@ mod tests {
),
left_flank_edit_costs: GapAffineAlignmentCostTable::new_zero(),
right_flank_edit_costs: GapAffineAlignmentCostTable::new_zero(),
offset_costs: CostFunction::try_from(
rq_qr_offset_costs: CostFunction::try_from(
(-20..=20)
.map(|i| (i, U64Cost::from(17 * u64::try_from(i + 21).unwrap())))
.collect::<Vec<_>>(),
)
.unwrap(),
rr_qq_offset_costs: CostFunction::try_from(
(-20..=20)
.map(|i| (i, U64Cost::from(17 * u64::try_from(i + 21).unwrap())))
.collect::<Vec<_>>(),
Expand Down
22 changes: 19 additions & 3 deletions lib_tsalign/src/a_star_aligner/template_switch_distance.rs
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Expand Up @@ -220,7 +220,8 @@ impl<Strategies: AlignmentStrategySelector> Node<Strategies> {
SubsequenceType: GenomeSequence<Strategies::Alphabet, SubsequenceType> + ?Sized,
>(
&'result self,
cost_increment: Strategies::Cost,
rq_qr_cost_increment: Strategies::Cost,
rr_qq_cost_increment: Strategies::Cost,
base_cost: &'result BaseCost<Strategies::Cost>,
context: &'result Context<SubsequenceType, Strategies>,
) -> impl 'result + Iterator<Item = Self> {
Expand All @@ -230,7 +231,10 @@ impl<Strategies: AlignmentStrategySelector> Node<Strategies> {
) {
unreachable!("This method is only called on primary nodes.")
}
debug_assert!(cost_increment < Strategies::Cost::max_value());
debug_assert!(
rq_qr_cost_increment < Strategies::Cost::max_value()
|| rr_qq_cost_increment < Strategies::Cost::max_value(),
);

self.node_data
.identifier
Expand All @@ -252,8 +256,20 @@ impl<Strategies: AlignmentStrategySelector> Node<Strategies> {
*template_switch_secondary,
*template_switch_direction,
);
let cost_increment = match (*template_switch_primary, *template_switch_secondary) {
(TemplateSwitchPrimary::Reference, TemplateSwitchSecondary::Query)
| (TemplateSwitchPrimary::Query, TemplateSwitchSecondary::Reference) => {
rq_qr_cost_increment
}
(TemplateSwitchPrimary::Reference, TemplateSwitchSecondary::Reference)
| (TemplateSwitchPrimary::Query, TemplateSwitchSecondary::Query) => {
rr_qq_cost_increment
}
};

(base_cost != Strategies::Cost::max_value()).then(|| {
(base_cost != Strategies::Cost::max_value()
&& cost_increment != Strategies::Cost::max_value())
.then(|| {
self.generate_successor(
identifier,
cost_increment + base_cost,
Expand Down
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