upgrade anndata-rs and pyo3

kaizhang · May 1, 2024 · f97216d · f97216d
1 parent 17537d6
commit f97216d
Show file tree

Hide file tree

Showing 12 changed files with 317 additions and 176 deletions.
diff --git a/snapatac2-core/Cargo.toml b/snapatac2-core/Cargo.toml
@@ -10,7 +10,7 @@ homepage = "https://github.com/"
 keywords = ["single-cell", "biology"]
 
 [dependencies]
-anndata = "0.3.2"
+anndata = "0.3.3"
 anyhow = "1.0"
 bigtools = { version = "0.4", features = ["read", "write"] }
 bincode = "1.3"
@@ -21,16 +21,16 @@ tokio = "1.34"
 hora = "0.1"
 kdtree = "0.7"
 itertools = "0.12"
-indexmap = "2.0"
+indexmap = "2.2"
 indicatif = {version = "0.17", features = ["rayon"] }
 lexical = "6.1"
 log = "0.4"
 ndarray = { version = "0.15", features = ["rayon"] }
 num = "0.4"
-noodles = { version = "0.64", features = ["core", "bam", "sam", "gff", "gtf"] }
+noodles = { version = "0.70", features = ["core", "bam", "sam", "gff", "gtf"] }
 nalgebra-sparse = "0.9"
-polars = { version = "0.37", features = ["ndarray", "dtype-categorical"] }
-rayon = "1.8"
+polars = { version = "0.39", features = ["ndarray", "dtype-categorical"] }
+rayon = "1.10"
 regex = "1.6"
 serde = "1.0"
 statrs = "0.16"

diff --git a/snapatac2-core/src/preprocessing/bam/mark_duplicates.rs b/snapatac2-core/src/preprocessing/bam/mark_duplicates.rs
@@ -333,7 +333,7 @@ impl FlagStat {
                 }
 
                 if !flags.is_unmapped() {
-                    if flags.is_properly_aligned() {
+                    if flags.is_properly_segmented() {
                         self.proper_pair += 1;
                     }
 
@@ -383,7 +383,7 @@ where
         flagstat.update(r);
         let flag = r.flags();
         let is_properly_aligned = !flag.is_supplementary() &&
-            (!is_paired || flag.is_properly_aligned());
+            (!is_paired || flag.is_properly_segmented());
         let flag_pass = !flag.intersects(flag_failed);
         let mapq_pass = mapq_filter.map_or(true, |min_q| {
             let q = r.mapping_quality().map_or(255, |x| x.get());