v2.6.2

snapatac2-core/Cargo.toml

@@ -14,8 +14,8 @@ anndata = "0.3.3"
 anyhow = "1.0"
 bigtools = { version = "0.4", features = ["read", "write"] }
 bincode = "1.3"
-bed-utils = "0.2"
-extsort = "0.4"
+bed-utils = "0.3"
+extsort = "0.5"
 flate2 = "1.0"
 tokio = "1.34"
 hora = "0.1"
@@ -36,4 +36,4 @@ serde = "1.0"
 statrs = "0.16"
 smallvec = "1.13"
 tempfile = "3.3"
-zstd = { version = "0.13", features = ["zstdmt"] }
+zstd = { version = "0.13", features = ["zstdmt"] }

snapatac2-core/src/preprocessing/bam/mark_duplicates.rs

@@ -28,7 +28,7 @@ use noodles::{
 use bed_utils::bed::{BEDLike, Strand};
 use std::collections::HashMap;
 use itertools::Itertools;
-use extsort::{sorter::Sortable, ExternalSorter};
+use extsort::{Sortable, ExternalSorter};
 use bincode;
 use log::warn;
 use rayon::prelude::ParallelSliceMut;
@@ -165,12 +165,16 @@ impl AlignmentInfo {
 }
 
 impl Sortable for AlignmentInfo {
-    fn encode<W: std::io::Write>(&self, writer: &mut W) {
-        bincode::serialize_into(writer, self).unwrap();
+    fn encode<W: std::io::Write>(&self, writer: &mut W) -> std::io::Result<()> {
+        bincode::serialize_into(writer, self).map_err(|e|
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 
-    fn decode<R: std::io::Read>(reader: &mut R) -> Option<Self> {
-        bincode::deserialize_from(reader).ok()
+    fn decode<R: std::io::Read>(reader: &mut R) -> std::io::Result<Self> {
+        bincode::deserialize_from(reader).map_err(|e|
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 }
 
@@ -420,6 +424,7 @@ where
                 .then_with(|| a.unclipped_start.cmp(&b.unclipped_start))
                 .then_with(|| a.unclipped_end.cmp(&b.unclipped_end))
             ).unwrap()
+            .map(|x| x.unwrap())
     }
 
     RecordGroups {

snapatac2-core/src/preprocessing/qc.rs

@@ -3,7 +3,7 @@ use anndata::data::CsrNonCanonical;
 use bed_utils::bed::{GenomicRange, BEDLike, tree::BedTree, ParseError, Strand};
 use anyhow::Result;
 use serde::{Serialize, Deserialize};
-use extsort::sorter::Sortable;
+use extsort::Sortable;
 use bincode;
 use smallvec::{SmallVec, smallvec};
 
@@ -22,13 +22,16 @@ pub struct Fragment {
 }
 
 impl Sortable for Fragment {
-    fn encode<W: std::io::Write>(&self, writer: &mut W) {
-        bincode::serialize_into(writer, self)
-            .unwrap_or_else(|e| panic!("Failed to serialize fragment: {}", e));
+    fn encode<W: std::io::Write>(&self, writer: &mut W) -> std::io::Result<()> {
+        bincode::serialize_into(writer, self).map_err(|e| 
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 
-    fn decode<R: std::io::Read>(reader: &mut R) -> Option<Self> {
-        bincode::deserialize_from(reader).ok()
+    fn decode<R: std::io::Read>(reader: &mut R) -> std::io::Result<Self> {
+        bincode::deserialize_from(reader).map_err(|e|
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 }
 
@@ -141,13 +144,16 @@ pub struct Contact {
 }
 
 impl Sortable for Contact {
-    fn encode<W: std::io::Write>(&self, writer: &mut W) {
-        bincode::serialize_into(writer, self)
-            .unwrap_or_else(|e| panic!("Failed to serialize fragment: {}", e));
+    fn encode<W: std::io::Write>(&self, writer: &mut W) -> std::io::Result<()> {
+        bincode::serialize_into(writer, self).map_err(|e|
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 
-    fn decode<R: std::io::Read>(reader: &mut R) -> Option<Self> {
-        bincode::deserialize_from(reader).ok()
+    fn decode<R: std::io::Read>(reader: &mut R) -> std::io::Result<Self> {
+        bincode::deserialize_from(reader).map_err(|e|
+            std::io::Error::new(std::io::ErrorKind::Other, e.to_string())
+        )
     }
 }
 

snapatac2-python/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "snapatac2"
-version = "2.6.2-dev0"
+version = "2.6.2"
 edition = "2021"
 authors = ["Kai Zhang <[email protected]>"]
 description = "Rust APIs"
@@ -15,9 +15,9 @@ snapatac2-core = { path = "../snapatac2-core" }
 anndata = "0.3.3"
 anndata-hdf5 = "0.2"
 pyanndata = "0.3.3"
-extsort = "0.4"
+extsort = "0.5"
 anyhow = "1.0"
-bed-utils = "0.2"
+bed-utils = "0.3"
 flate2 = "1.0"
 itertools = "0.12"
 indicatif = "0.17"

snapatac2-python/src/preprocessing.rs

@@ -109,7 +109,7 @@ pub(crate) fn import_fragments(
             f
     });
     let sorted_fragments: Box<dyn Iterator<Item = Fragment>> = if !fragment_is_sorted_by_name {
-        Box::new(bed::sort_bed_by_key(fragments, |x| x.barcode.clone(), tempdir))
+        Box::new(bed::sort_bed_by_key(fragments, |x| x.barcode.clone(), tempdir).map(|x| x.unwrap()))
     } else {
         Box::new(fragments)
     };
@@ -164,6 +164,7 @@ pub(crate) fn import_contacts(
             .with_sort_dir(tmp.path().to_path_buf())
             .with_parallel_sort()
             .sort_by_key(contacts, |x| x.barcode.clone()).unwrap()
+            .map(|x| x.unwrap())
         )
     } else {
         Box::new(contacts)