tsalign 2.1.2__tar.gz → 4.0.0__tar.gz

{tsalign-2.1.2 → tsalign-4.0.0}/Cargo.lock

@@ -417,7 +417,7 @@ checksum = "e6d5a32815ae3f33302d95fdcb2ce17862f8c65363dcfd29360480ba1001fc9c"
 
 [[package]]
 name = "generic_a_star"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "binary-heap-plus",
  "compare",
@@ -548,7 +548,7 @@ checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe"
 
 [[package]]
 name = "lib_ts_chainalign"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "binary-heap-plus",
  "bincode",
@@ -568,7 +568,7 @@ dependencies = [
 
 [[package]]
 name = "lib_tsalign"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "binary-heap-plus",
  "compact-genome",
@@ -589,7 +589,7 @@ dependencies = [
 
 [[package]]
 name = "lib_tsshow"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "ena",
  "itertools",
@@ -804,7 +804,7 @@ dependencies = [
 
 [[package]]
 name = "py_lib_tsalign"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "compact-genome",
  "lib_tsalign",
@@ -1008,7 +1008,7 @@ dependencies = [
 
 [[package]]
 name = "seed_chain"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "compact-genome",
  "generic_a_star",
@@ -1360,7 +1360,7 @@ checksum = "2b939c825d0c4295ac520f7b479927c1e5b458c9107a9d6f5ba65bc867bb93a5"
 
 [[package]]
 name = "tsalign"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "anyhow",
  "bincode",
@@ -1381,7 +1381,7 @@ dependencies = [
 
 [[package]]
 name = "tsalign-tests"
-version = "2.1.2"
+version = "4.0.0"
 dependencies = [
  "anyhow",
  "clap",

{tsalign-2.1.2 → tsalign-4.0.0}/Cargo.toml

@@ -18,5 +18,9 @@ num-traits = "0.2.19"
 rustc-hash = "2.1.1"
 binary-heap-plus = "0.5.0"
 
+[profile.dev]
+debug = 1 # or "line-tables-only" instead of full debug info
+split-debuginfo = "unpacked" # Keeps symbols out of the main object file
+
 [profile.release]
-debug = true
+debug = 1

{tsalign-2.1.2 → tsalign-4.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tsalign
-Version: 2.1.2
+Version: 4.0.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -104,9 +104,9 @@ from tsalign import align, TemplateSwitchEntranceOp, TemplateSwitchExitOp
 result = align(reference, query)
 for count, op in result.alignments():
     if isinstance(op, TemplateSwitchEntranceOp):
-        print(f"Template switch: {op.direction}, primary={op.primary}, offset={op.first_offset}")
+        print(f"Template switch: {op.direction}, descendant={op.descendant}, offset={op.first_offset}")
     elif isinstance(op, TemplateSwitchExitOp):
-        print(f"Exit, anti-primary gap: {op.anti_primary_gap}")
+        print(f"Exit, anti-descendant gap: {op.anti_descendant_gap}")
     else:
         # SimpleAlignmentOp — a basic edit in the primary or secondary track
         print(f"{count}x {op.kind}")

{tsalign-2.1.2/python_bindings → tsalign-4.0.0}/README.md

@@ -95,9 +95,9 @@ from tsalign import align, TemplateSwitchEntranceOp, TemplateSwitchExitOp
 result = align(reference, query)
 for count, op in result.alignments():
     if isinstance(op, TemplateSwitchEntranceOp):
-        print(f"Template switch: {op.direction}, primary={op.primary}, offset={op.first_offset}")
+        print(f"Template switch: {op.direction}, descendant={op.descendant}, offset={op.first_offset}")
     elif isinstance(op, TemplateSwitchExitOp):
-        print(f"Exit, anti-primary gap: {op.anti_primary_gap}")
+        print(f"Exit, anti-descendant gap: {op.anti_descendant_gap}")
     else:
         # SimpleAlignmentOp — a basic edit in the primary or secondary track
         print(f"{count}x {op.kind}")

{tsalign-2.1.2 → tsalign-4.0.0}/generic_a_star/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "generic_a_star"
 description = "A generic implementation of the A* algorithm"
-version = "2.1.2"
+version = "4.0.0"
 edition.workspace = true
 rust-version.workspace = true
 license.workspace = true

{tsalign-2.1.2 → tsalign-4.0.0}/lib_tsalign/Cargo.toml

@@ -2,7 +2,7 @@
 name = "lib_tsalign"
 description = "A sequence-to-sequence aligner that accounts for template switches"
 authors = ["Sebastian Schmidt <sebastian.schmidt@helsinki.fi>"]
-version = "2.1.2"
+version = "4.0.0"
 license.workspace = true
 edition.workspace = true
 rust-version.workspace = true
@@ -26,9 +26,9 @@ thiserror = "2.0.3"
 num-traits.workspace = true
 serde = { workspace = true, features = ["derive"], optional = true }
 noisy_float = { version = "0.2.0" }
-generic_a_star = { version = "2.1.2", path = "../generic_a_star" }
+generic_a_star = { version = "4.0.0", path = "../generic_a_star" }
 log.workspace = true
 rustc-hash = "2.1.1"
-seed_chain = { version = "2.1.2", path = "../seed_chain" }
+seed_chain = { version = "4.0.0", path = "../seed_chain" }
 extend_map = "0.14.3"
 template-switch-error-free-inners = "0.1.1"

{tsalign-2.1.2 → tsalign-4.0.0}/lib_tsalign/src/a_star_aligner/alignment_geometry.rs

@@ -17,6 +17,18 @@ pub struct AlignmentCoordinates {
 }
 
 impl AlignmentRange {
+    pub fn new(
+        reference_offset: usize,
+        query_offset: usize,
+        reference_limit: usize,
+        query_limit: usize,
+    ) -> Self {
+        Self {
+            offset: AlignmentCoordinates::new(reference_offset, query_offset),
+            limit: AlignmentCoordinates::new(reference_limit, query_limit),
+        }
+    }
+
     pub fn new_complete(reference: usize, query: usize) -> Self {
         Self {
             offset: AlignmentCoordinates::new_zero(),
@@ -102,6 +114,16 @@ impl AlignmentRange {
             ),
         ))
     }
+
+    #[must_use]
+    pub fn with_offset(&self, offset: AlignmentCoordinates) -> Self {
+        Self::new_offset_limit(offset, self.limit)
+    }
+
+    #[must_use]
+    pub fn with_limit(&self, limit: AlignmentCoordinates) -> Self {
+        Self::new_offset_limit(self.offset, limit)
+    }
 }
 
 impl AlignmentCoordinates {
@@ -112,6 +134,14 @@ impl AlignmentCoordinates {
     pub fn new_zero() -> Self {
         Self::new(0, 0)
     }
+
+    pub fn reference(&self) -> usize {
+        self.reference
+    }
+
+    pub fn query(&self) -> usize {
+        self.query
+    }
 }
 
 impl Display for AlignmentRange {

{tsalign-2.1.2 → tsalign-4.0.0}/lib_tsalign/src/a_star_aligner/alignment_result/alignment/stream.rs

@@ -2,7 +2,7 @@ use std::{collections::VecDeque, iter};
 
 use crate::a_star_aligner::{
     alignment_result::alignment::Alignment,
-    template_switch_distance::{AlignmentType, TemplateSwitchPrimary},
+    template_switch_distance::{AlignmentType, TemplateSwitchDescendant},
 };
 
 #[derive(Debug, Clone)]
@@ -20,7 +20,7 @@ pub struct AlignmentStream {
 pub struct AlignmentStreamCoordinates {
     reference: usize,
     query: usize,
-    template_switch_primary: Option<TemplateSwitchPrimary>,
+    template_switch_descendant: Option<TemplateSwitchDescendant>,
 }
 
 impl AlignmentStream {
@@ -176,8 +176,9 @@ impl AlignmentStream {
             AlignmentType::TemplateSwitchEntrance { .. }
             | AlignmentType::TemplateSwitchExit { .. }
             | AlignmentType::Root
+            | AlignmentType::AlternativeStart { .. }
             | AlignmentType::SecondaryRoot
-            | AlignmentType::PrimaryReentry => 0,
+            | AlignmentType::PrimaryReentry { .. } => 0,
             AlignmentType::PrimaryShortcut { .. } => {
                 unreachable!("Shortcut alignments are not supported for show")
             }
@@ -190,7 +191,7 @@ impl AlignmentStreamCoordinates {
         Self {
             reference: reference_offset,
             query: query_offset,
-            template_switch_primary: None,
+            template_switch_descendant: None,
         }
     }
 
@@ -210,42 +211,60 @@ impl AlignmentStreamCoordinates {
             | AlignmentType::PrimaryMatch
             | AlignmentType::PrimaryFlankSubstitution
             | AlignmentType::PrimaryFlankMatch => (1, 1),
-            AlignmentType::TemplateSwitchEntrance { primary, .. } => {
+            AlignmentType::TemplateSwitchEntrance { descendant, .. } => {
                 assert!(
-                    self.template_switch_primary.is_none(),
+                    self.template_switch_descendant.is_none(),
                     "Encountered template switch entrance within template switch"
                 );
-                self.template_switch_primary = Some(primary);
+                self.template_switch_descendant = Some(descendant);
                 (0, 0)
             }
             AlignmentType::SecondaryInsertion
             | AlignmentType::SecondarySubstitution
-            | AlignmentType::SecondaryMatch => match self.template_switch_primary.unwrap() {
-                TemplateSwitchPrimary::Reference => (1, 0),
-                TemplateSwitchPrimary::Query => (0, 1),
+            | AlignmentType::SecondaryMatch => match self.template_switch_descendant.unwrap() {
+                TemplateSwitchDescendant::Reference => (1, 0),
+                TemplateSwitchDescendant::Query => (0, 1),
             },
-            AlignmentType::TemplateSwitchExit { anti_primary_gap } => {
-                let Some(template_switch_primary) = self.template_switch_primary.take() else {
+            AlignmentType::TemplateSwitchExit {
+                anti_descendant_gap,
+            } => {
+                let Some(template_switch_descendant) = self.template_switch_descendant.take()
+                else {
                     panic!(
                         "Encountered template switch exit without first encountering a template switch entrance"
                     )
                 };
-                match template_switch_primary {
-                    TemplateSwitchPrimary::Reference => {
+                match template_switch_descendant {
+                    TemplateSwitchDescendant::Reference => {
                         self.query =
-                            usize::try_from(self.query as isize + anti_primary_gap).unwrap()
+                            usize::try_from(self.query as isize + anti_descendant_gap).unwrap()
                     }
-                    TemplateSwitchPrimary::Query => {
+                    TemplateSwitchDescendant::Query => {
                         self.reference =
-                            usize::try_from(self.reference as isize + anti_primary_gap).unwrap()
+                            usize::try_from(self.reference as isize + anti_descendant_gap).unwrap()
                     }
                 }
                 (0, 0)
             }
+            AlignmentType::AlternativeStart {
+                reference_index,
+                query_index,
+            } => {
+                assert_eq!(self.reference, reference_index);
+                assert_eq!(self.query, query_index);
+                (0, 0)
+            }
+            AlignmentType::PrimaryReentry {
+                reference_index,
+                query_index,
+            } => {
+                assert_eq!(self.reference, reference_index);
+                assert_eq!(self.query, query_index);
+                (0, 0)
+            }
             AlignmentType::SecondaryDeletion
             | AlignmentType::Root
-            | AlignmentType::SecondaryRoot
-            | AlignmentType::PrimaryReentry => (0, 0),
+            | AlignmentType::SecondaryRoot => (0, 0),
             AlignmentType::PrimaryShortcut { .. } => {
                 unreachable!("Shortcut alignments are not supported for show")
             }