Update to v0.12.7

PacificBiosciences · Oct 23, 2024 · 4a790c6 · 4a790c6
1 parent 5f0b2b6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Change Log
 
+## v0.12.7 - 2024-10-23
+
+### Fixed
+
+- Fix "Illegal Instruction" error reported for some use cases (github #3)
+  - Removed gcc native cpu optimization in WFA2-lib believed to be causing this issue
+  - Added additional `--debug` output to discover mode contig alignment logic
+
 ## v0.12.6 - 2024-10-15
 
 ### Fixed

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "sawfish"
-version = "0.12.6"
+version = "0.12.7"
 authors = ["Chris Saunders <[email protected]>"]
 description = "Structural variant analysis for mapped PacBio HiFi reads"
 edition = "2021"

diff --git a/LICENSE-THIRDPARTY.json b/LICENSE-THIRDPARTY.json
@@ -125,15 +125,6 @@
     "license_file": null,
     "description": "Automatically generates Rust FFI bindings to C and C++ libraries."
   },
-  {
-    "name": "bindgen",
-    "version": "0.70.1",
-    "authors": "Jyun-Yan You <[email protected]>|Emilio Cobos Álvarez <[email protected]>|Nick Fitzgerald <[email protected]>|The Servo project developers",
-    "repository": "https://github.com/rust-lang/rust-bindgen",
-    "license": "BSD-3-Clause",
-    "license_file": null,
-    "description": "Automatically generates Rust FFI bindings to C and C++ libraries."
-  },
   {
     "name": "bio",
     "version": "2.0.3",
@@ -782,6 +773,15 @@
     "license_file": null,
     "description": "Format time and duration in chrono, std::time and time as HH:MM:SS and HH:MM:SS.xxx"
   },
+  {
+    "name": "home",
+    "version": "0.5.9",
+    "authors": "Brian Anderson <[email protected]>",
+    "repository": "https://github.com/rust-lang/cargo",
+    "license": "Apache-2.0 OR MIT",
+    "license_file": null,
+    "description": "Shared definitions of home directories."
+  },
   {
     "name": "hts-sys",
     "version": "2.1.4",
@@ -1576,7 +1576,7 @@
   },
   {
     "name": "sawfish",
-    "version": "0.12.6",
+    "version": "0.12.7",
     "authors": "Chris Saunders <[email protected]>",
     "repository": null,
     "license": null,
@@ -2141,6 +2141,15 @@
     "license_file": null,
     "description": null
   },
+  {
+    "name": "which",
+    "version": "4.4.2",
+    "authors": "Harry Fei <[email protected]>",
+    "repository": "https://github.com/harryfei/which-rs.git",
+    "license": "MIT",
+    "license_file": null,
+    "description": "A Rust equivalent of Unix command \"which\". Locate installed executable in cross platforms."
+  },
   {
     "name": "wide",
     "version": "0.7.28",

diff --git a/docs/user_guide.md b/docs/user_guide.md
@@ -67,7 +67,7 @@ Sawfish analyzes samples in 2 steps:
 
 ### Calling SVs on one sample
 
-To call SVs in one sample, run `discover` on the the mapped sample bam, and then run joint call on the output directory of the discover step.
+To call SVs in one sample, run `discover` on the mapped sample bam, and then run joint call on the output directory of the discover step.
 
 The following example shows how this is done for a mapped sample bam named `HG002.GRCh38.bam`, using 16 threads for both the `discover` and the `joint-call` steps.
 

diff --git a/src/large_variant_output.rs b/src/large_variant_output.rs
@@ -722,7 +722,7 @@ fn get_bnd_alt_seq(
     ))
 }
 
-/// * vcf - Used to link the corresponding bam header to the the vcf record
+/// * vcf - Used to link the corresponding bam header to the vcf record
 ///
 #[allow(clippy::too_many_arguments)]
 fn convert_refined_sv_to_bnd_vcf_record(

diff --git a/src/refine_sv/align/mod.rs b/src/refine_sv/align/mod.rs
@@ -28,6 +28,7 @@ use crate::expected_ploidy::SVLocusPloidy;
 use crate::genome_ref_utils::get_ref_segment_seq;
 use crate::genome_segment::GenomeSegment;
 use crate::int_range::{get_overlap_range, IntRange};
+use crate::log_utils::debug_msg;
 use crate::refine_sv::{AnnotatedOverlappingHaplotype, RefinedSVExt, SVScoreInfo};
 use crate::simple_alignment::{clip_alignment_ref_edges, SimpleAlignment};
 use crate::sv_group::{
@@ -417,17 +418,13 @@ fn align_single_ref_region_assemblies(
     let is_any_filter = filter_all_overlapping_svs || filter_close_overlapping_svs;
 
     let debug = false;
-    if debug {
-        eprintln!("SingleRef cluster id {cluster_index} - filter_all_overlapping_svs: {filter_all_overlapping_svs} filter_close_overlapping_svs: {filter_close_overlapping_svs}");
-    }
+    debug_msg!(debug, "SingleRef Cluster {cluster_index}: filter_all_overlapping_svs: {filter_all_overlapping_svs} filter_close_overlapping_svs: {filter_close_overlapping_svs}");
 
     let mut overlapping_haplotypes = Vec::new();
 
     for (assembly_index, assembly) in assemblies.iter().enumerate() {
         if assembly.supporting_read_count() < refine_settings.min_assembly_read_support {
-            if debug {
-                eprintln!("SingleRef cluster/contig id {cluster_index}/{assembly_index} - filtered for low read support: {}", assembly.supporting_read_count());
-            }
+            debug_msg!(debug, "SingleRef cluster/contig: {cluster_index}/{assembly_index} - filtered for low read support: {}", assembly.supporting_read_count());
             continue;
         }
 
@@ -440,20 +437,17 @@ fn align_single_ref_region_assemblies(
         {
             (score, Some(x)) => (score, x),
             (_, None) => {
-                if debug {
-                    eprintln!("SingleRef cluster/contig id {cluster_index}/{assembly_index} - filtered for poor contig to ref alignment");
-                }
+                debug_msg!(debug, "SingleRef cluster/contig: {cluster_index}/{assembly_index} - filtered for poor contig to ref alignment");
                 // TODO add warning or statistics to track these filtration cases
                 continue;
             }
         };
-        if debug {
-            eprintln!("SingleRef cluster/contig id {cluster_index}/{assembly_index} - assembly_contig_to_chrom_segment_alignment: {:?}", assembly_contig_to_chrom_segment_alignment);
-            eprintln!(
-                "SingleRef cluster/contig ids {cluster_index}/{assembly_index} - alignment_score {}",
-                alignment_score
-            );
-        }
+        debug_msg!(debug, "SingleRef cluster/contig: {cluster_index}/{assembly_index} - assembly_contig_to_chrom_segment_alignment: {:?}", assembly_contig_to_chrom_segment_alignment);
+        debug_msg!(
+            debug,
+            "SingleRef cluster/contig: {cluster_index}/{assembly_index} - alignment_score {}",
+            alignment_score
+        );
 
         // Starting reference position of the assembly alignment
         let chrom_pos =