From f99b913bd7cae564c62028631c3a35c4d621d692 Mon Sep 17 00:00:00 2001
From: Rob Patro <rob@newton>
Date: Wed, 13 Nov 2024 22:12:14 -0500
Subject: [PATCH] update deps, fix unique counting in bam mode

---
 Cargo.toml                | 24 ++++++++++++------------
 src/alignment_parser.rs   | 12 ++++++------
 src/bulk.rs               |  6 +++---
 src/util/oarfish_types.rs |  6 +++++-
 4 files changed, 26 insertions(+), 22 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 3486b26..12e63d5 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -25,13 +25,13 @@ categories = ["command-line-utilities", "science"]
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
-seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.2" }
-anyhow = "1.0.86"
-bstr = "1.10.0"
+seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.3" }
+anyhow = "1.0.93"
+bstr = "1.11.0"
 bio-types = { version = "1.0.4", features = ["serde"] }
-clap = { version = "4.5.16", features = ["derive"] }
-noodles-bam = "0.66.0"
-noodles-sam = "0.63.0"
+clap = { version = "4.5.21", features = ["derive"] }
+noodles-bam = "0.70.0"
+noodles-sam = "0.66.0"
 num-format = "0.4.4"
 lz4 = "1.28.0"
 either = "1.13.0"
@@ -44,9 +44,9 @@ statrs = "0.17"
 csv = "1.3"
 serde = { version = "1", features = ["derive"] }
 itertools = "0.13.0"
-serde_json = "1.0.127"
+serde_json = "1.0.132"
 path-tools = "0.1.0"
-atomic_float = "1.0.0"
+atomic_float = "1.1.0"
 sendable-swapvec = "0.4.3"
 rand = "0.8.5"
 arrow2 = { version = "0.18.0", features = [
@@ -56,12 +56,12 @@ arrow2 = { version = "0.18.0", features = [
   "io_parquet_snappy",
 ] }
 kders = { git = "https://github.com/COMBINE-lab/kde-rs.git", branch = "dev", version = "0.1.1" }
-noodles-bgzf = { version = "0.32.0" }
+noodles-bgzf = { version = "0.33.0" }
 crossbeam = { version = "0.8.4", features = [
   "crossbeam-queue",
   "crossbeam-channel",
 ] }
-sprs = "0.11.1"
+sprs = "0.11.2"
 minimap2-sys = { version = "0.1.19" }
 # rely on minimap2-temp until upstream version is pushed
 # make sure relevant changes are in upstream PR
@@ -69,8 +69,8 @@ minimap2-temp = { version = "0.1.32" }
 # alternative sources for dev
 #minimap2-temp = { version = "0.1.20", git = "https://github.com/rob-p/minimap2-rs.git", branch = "alignment-score" }
 #minimap2 = { version = "0.1.20", git = "https://github.com/jguhlin/minimap2-rs.git", branch = "alignment-score" }
-needletail = "0.5.1"
-indicatif = "0.17.8"
+needletail = "0.6.0"
+indicatif = "0.17.9"
 rustc-hash = "2.0.0"
 
 [[bin]]
diff --git a/src/alignment_parser.rs b/src/alignment_parser.rs
index f177954..e2ad2f5 100644
--- a/src/alignment_parser.rs
+++ b/src/alignment_parser.rs
@@ -309,9 +309,9 @@ pub fn parse_alignments<R: io::BufRead>(
                 if !prev_read.is_empty() {
                     if store.add_group(txps, &mut records_for_read) {
                         add_read_name(&records_for_read);
-                    }
-                    if records_for_read.len() == 1 {
-                        store.inc_unique_alignments();
+                        if records_for_read.len() == 1 {
+                            store.inc_unique_alignments();
+                        }
                     }
                     records_for_read.clear();
                 }
@@ -343,9 +343,9 @@ pub fn parse_alignments<R: io::BufRead>(
         // if we are using read names and we added the group here
         if store.add_group(txps, &mut records_for_read) {
             add_read_name(&records_for_read);
-        }
-        if records_for_read.len() == 1 {
-            store.inc_unique_alignments();
+            if records_for_read.len() == 1 {
+                store.inc_unique_alignments();
+            }
         }
         records_for_read.clear();
     }
diff --git a/src/bulk.rs b/src/bulk.rs
index a502036..4d533b6 100644
--- a/src/bulk.rs
+++ b/src/bulk.rs
@@ -534,15 +534,15 @@ pub fn quantify_bulk_alignments_raw_reads(
                         None
                     };
 
-                    if ag.len() == 1 {
-                        store.inc_unique_alignments();
-                    }
                     if store.add_filtered_group(ag, as_probs, txps_mut) {
                         if let Some(ref mut nvec) = name_vec {
                             let read_name = read_name_opt.unwrap_or(EMPTY_READ_NAME.to_string());
                             nvec.push(read_name)
                                 .expect("cannot push name to read name vector");
                         }
+                        if ag.len() == 1 {
+                            store.inc_unique_alignments();
+                        }
                     }
                 }
             }
diff --git a/src/util/oarfish_types.rs b/src/util/oarfish_types.rs
index fccd8de..2e6bee0 100644
--- a/src/util/oarfish_types.rs
+++ b/src/util/oarfish_types.rs
@@ -186,7 +186,11 @@ impl<T: NoodlesAlignmentLike + noodles_sam::alignment::Record> AlnRecordLike for
     }
 
     fn aln_span(&self) -> Option<usize> {
-        self.alignment_span().expect("valid span")
+        // NOTE: The transpose here is because noodles_sam
+        // switched from returning Result<Option<usize>> to
+        // Option<Result<usize>> --- think if there is a
+        // better way to handle the new return type directly
+        self.alignment_span().transpose().expect("valid span")
     }
 
     fn aln_score(&self) -> Option<i64> {