Merge branch 'master' into phylogeny_tools

rust-bio · Apr 10, 2024 · dd2d2cd · dd2d2cd
2 parents b0fd27d + 7913136
commit dd2d2cd
Show file tree

Hide file tree

Showing 56 changed files with 981 additions and 593 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: cargo
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,160 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+### [0.42.2](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.42.1...v0.42.2) (2024-04-10)
+
+
+### Miscellaneous Chores
+
+* release 0.42.2 ([a1793ea](https://www.github.com/rust-bio/rust-bio-tools/commit/a1793ea7e7fe68d05e5d05c714213ad474581e70))
+
+### [0.42.1](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.42.0...v0.42.1) (2023-07-24)
+
+
+### Bug Fixes
+
+* consensus reads: correct handling of read orientation ([#252](https://www.github.com/rust-bio/rust-bio-tools/issues/252)) ([9ca5f18](https://www.github.com/rust-bio/rust-bio-tools/commit/9ca5f1817dd1e6194adb8d1ed8a805725f48e161))
+
+## [0.42.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.41.0...v0.42.0) (2023-01-18)
+
+
+### Features
+
+* consensus reads - move record ids to description field ([#250](https://www.github.com/rust-bio/rust-bio-tools/issues/250)) ([f7d683b](https://www.github.com/rust-bio/rust-bio-tools/commit/f7d683b11964d9fb992827d59dd0d9a645c79cd5))
+
+## [0.41.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.40.0...v0.41.0) (2022-08-19)
+
+
+### Features
+
+* Remove duplicate marks from consensus records ([#247](https://www.github.com/rust-bio/rust-bio-tools/issues/247)) ([692eb04](https://www.github.com/rust-bio/rust-bio-tools/commit/692eb041683ac898277628b140da13e88ec40449))
+
+## [0.40.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.39.1...v0.40.0) (2022-07-21)
+
+
+### Features
+
+* Enable printing FILTER field for vcf-to-txt ([#242](https://www.github.com/rust-bio/rust-bio-tools/issues/242)) ([13bef65](https://www.github.com/rust-bio/rust-bio-tools/commit/13bef659588d9c7cfd81eaff459234c5659a99b8))
+
+### [0.39.1](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.39.0...v0.39.1) (2022-06-14)
+
+
+### Bug Fixes
+
+* Handle empty sequences for bam-anonymize ([#241](https://www.github.com/rust-bio/rust-bio-tools/issues/241)) ([039ed92](https://www.github.com/rust-bio/rust-bio-tools/commit/039ed92665b094e8ebcbe42bf955496891d5d962))
+* Improved message if error occurred during FORMAT parsing in vcf-to-txt ([#243](https://www.github.com/rust-bio/rust-bio-tools/issues/243)) ([4231371](https://www.github.com/rust-bio/rust-bio-tools/commit/423137126bf904001ca871f195620ed47821af91))
+* vcfsplit BND record ordering ([#244](https://www.github.com/rust-bio/rust-bio-tools/issues/244)) ([9b7ae9a](https://www.github.com/rust-bio/rust-bio-tools/commit/9b7ae9a023ad84467131201d837bef3987306d2a))
+
+## [0.39.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.38.3...v0.39.0) (2022-02-21)
+
+
+### Features
+
+* Make annotation header available for customized reports ([#238](https://www.github.com/rust-bio/rust-bio-tools/issues/238)) ([e8fc664](https://www.github.com/rust-bio/rust-bio-tools/commit/e8fc664536ca6313a391dbb4ba955317e7ac50e6))
+
+### [0.38.3](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.38.2...v0.38.3) (2022-02-09)
+
+
+### Bug Fixes
+
+* Fix vcf-report allele frequency heatmap width ([#236](https://www.github.com/rust-bio/rust-bio-tools/issues/236)) ([6f119d3](https://www.github.com/rust-bio/rust-bio-tools/commit/6f119d3bab34594029a846172e29623fb9ed71aa))
+* Fix vcf-report read plot height when using --max-read-depth ([#235](https://www.github.com/rust-bio/rust-bio-tools/issues/235)) ([4350a1a](https://www.github.com/rust-bio/rust-bio-tools/commit/4350a1a3887d7f22e16de8ed8944981d138982d6))
+
+### [0.38.2](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.38.1...v0.38.2) (2022-01-14)
+
+
+### Bug Fixes
+
+* add popper in csv report ([#233](https://www.github.com/rust-bio/rust-bio-tools/issues/233)) ([a095755](https://www.github.com/rust-bio/rust-bio-tools/commit/a0957551e39928a510c7abd408378c274a3b5c33))
+
+### [0.38.1](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.38.0...v0.38.1) (2022-01-06)
+
+
+### Bug Fixes
+
+* Report 1-based position in vcf-report log messages ([#231](https://www.github.com/rust-bio/rust-bio-tools/issues/231)) ([bcf6260](https://www.github.com/rust-bio/rust-bio-tools/commit/bcf62609b52578a30a21a42971e0001701941681))
+
+## [0.38.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.37.0...v0.38.0) (2021-12-25)
+
+
+### Features
+
+* Add aux field to tooltip ([#226](https://www.github.com/rust-bio/rust-bio-tools/issues/226)) ([cfc8fe5](https://www.github.com/rust-bio/rust-bio-tools/commit/cfc8fe572fbc2e498d3d3cc0fe0de9e320b773d1))
+
+
+### Bug Fixes
+
+* Apply latest clippy lints ([#227](https://www.github.com/rust-bio/rust-bio-tools/issues/227)) ([d1a60cc](https://www.github.com/rust-bio/rust-bio-tools/commit/d1a60cc8876eb8ea2b6cffb21bdcee44a00d2dc4))
+
+## [0.37.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.36.0...v0.37.0) (2021-12-19)
+
+
+### Features
+
+* anonymize bam - adapt mandatory and aux fields ([#219](https://www.github.com/rust-bio/rust-bio-tools/issues/219)) ([e6ffdea](https://www.github.com/rust-bio/rust-bio-tools/commit/e6ffdea140704e305d8b30213c57d76bf7841fc2))
+
+## [0.36.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.35.0...v0.36.0) (2021-12-15)
+
+
+### Features
+
+* Use Feature before HGVSg for level 1 naming ([#224](https://www.github.com/rust-bio/rust-bio-tools/issues/224)) ([4377e42](https://www.github.com/rust-bio/rust-bio-tools/commit/4377e428e9bca2b806e666a8234da35e027fd523))
+* Warn instead of panic for missing HGVSg values in vcf-report ([#220](https://www.github.com/rust-bio/rust-bio-tools/issues/220)) ([5f16505](https://www.github.com/rust-bio/rust-bio-tools/commit/5f1650506fb502548e07d2756ff99557bb562580))
+
+
+### Bug Fixes
+
+* Fix possible broken link to third stage of vcf-report ([#221](https://www.github.com/rust-bio/rust-bio-tools/issues/221)) ([66299d2](https://www.github.com/rust-bio/rust-bio-tools/commit/66299d2e0e5ac96f67db8fcf4fef7834c2a2de05))
+
+## [0.35.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.34.0...v0.35.0) (2021-12-14)
+
+
+### Features
+
+* Add --annotation-field option to vcf-report ([#211](https://www.github.com/rust-bio/rust-bio-tools/issues/211)) ([29719d5](https://www.github.com/rust-bio/rust-bio-tools/commit/29719d51f0169de39570c6715af5b45336691ebb))
+
+
+### Bug Fixes
+
+* add missing js-file to vcf-report ([#212](https://www.github.com/rust-bio/rust-bio-tools/issues/212)) ([55b3166](https://www.github.com/rust-bio/rust-bio-tools/commit/55b3166516b6f369577df74f8cc020fbe9629721))
+* release version ([5de5480](https://www.github.com/rust-bio/rust-bio-tools/commit/5de548073816dc46ec68ad352c3b91a738971e20))
+* vcf-report tests ([#215](https://www.github.com/rust-bio/rust-bio-tools/issues/215)) ([b3e45b3](https://www.github.com/rust-bio/rust-bio-tools/commit/b3e45b3a290bfea7d1553ff34e186f1f870c6e02))
+
+
+### Miscellaneous Chores
+
+* release 0.33.2 ([10d2446](https://www.github.com/rust-bio/rust-bio-tools/commit/10d24469bfc5ea72ea385e82537e1fb52ca8f364))
+
+## [0.34.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.33.1...v0.34.0) (2021-12-11)
+
+### Features
+
+* Add --annotation-field option to vcf-report ([#211](https://github.com/rust-bio/rust-bio-tools/pull/211)) ([29719d5](https://github.com/rust-bio/rust-bio-tools/commit/29719d51f0169de39570c6715af5b45336691ebb))
+
+
+### Bug Fixes
+
+* add missing js-file to vcf-report ([#212](https://github.com/rust-bio/rust-bio-tools/pull/212)) ([55b3166](https://github.com/rust-bio/rust-bio-tools/commit/55b3166516b6f369577df74f8cc020fbe9629721))
+
+## [0.33.1](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.33.0...v0.33.1) (2021-12-07)
+
+
+### Features
+
+* Improve gene search for vcf-report ([#209](https://www.github.com/rust-bio/rust-bio-tools/issues/209)) ([cbeaff5](https://www.github.com/rust-bio/rust-bio-tools/commit/cbeaff5a79bf19fb745fa0e15505d5c41a9a6dd5))
+
+## [0.33.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.32.0...v0.33.0) (2021-12-06)
+
+
+### Features
+
+* Updates and fixes for vcf-report ([#207](https://www.github.com/rust-bio/rust-bio-tools/issues/207)) ([e19b4fb](https://www.github.com/rust-bio/rust-bio-tools/commit/e19b4fb4e3d935bfa5f41796dc23669a903563dc))
+
+
+### Bug Fixes
+
+* Add error messages for missing annotations ([#206](https://www.github.com/rust-bio/rust-bio-tools/issues/206)) ([6210dd2](https://www.github.com/rust-bio/rust-bio-tools/commit/6210dd22749c4cff818724f1a24dc6d8f104c927))
+
 ## [0.32.0](https://www.github.com/rust-bio/rust-bio-tools/compare/v0.31.0...v0.32.0) (2021-12-01)
 
 

diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "rust-bio-tools"
-version = "0.32.0"
+version = "0.42.2"
 authors = ["Johannes Köster <[email protected]>", "Erik Clarke <[email protected]>"]
 description = "A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio."
 license-file = "LICENSE.md"
@@ -16,7 +16,7 @@ indicatif = "0.11"
 itertools = "0.9"
 log = "0.4.6"
 fern = "0.5.7"
-rust-htslib = "0.38"
+rust-htslib = "0.46.0"
 csv = "1.0.2"
 rustc-serialize = "0.3"
 newtype_derive = "0.1"
@@ -28,19 +28,19 @@ serde_derive = "1.0"
 serde_json = "1.0"
 uuid = { version = "0.7", features = ["v4"] }
 tempfile = "3.0"
-rocksdb = "0.17"
+rocksdb = "0.19"
 ordered-float = "0.5"
 flate2 = "1.0.5"
 streaming-stats =  "0.2.2"
-GSL = "1.1.0"
+GSL = "7.0.0"
 bio-types = ">=0.5.1"
 derive-new = "0.5"
 reqwest = "0.9"
 regex = "1.3"
 tera = "1"
 jsonm = "0.1.4"
 chrono = "0.4"
-xlsxwriter = {version = "0.3.5", features= ["use-openssl-md5", "no-md5"]}
+xlsxwriter = {version = "0.6", features= ["use-openssl-md5", "no-md5"]}
 lazy_static = "1.4"
 anyhow = "1"
 thiserror = "1"
@@ -56,4 +56,13 @@ path = "src/main.rs"
 
 
 [features]
-default = ["GSL/v2"]
+default = ["GSL/v2_1"]
+
+[profile.release]
+codegen-units = 1
+lto = "fat"
+
+[profile.develop]
+codegen-units = 128
+inherits = "release"
+lto = false
diff --git a/README.md b/README.md
@@ -27,6 +27,14 @@ For a list of changes, take a look at the [CHANGELOG](CHANGELOG.md).
 
 ## Installation
 
+### Requirements
+
+Rust-Bio-Tools depends [rgsl](https://docs.rs/GSL/*/rgsl/) which needs [GSL](https://www.gnu.org/software/gsl/) to be installed:
+
+- Ubuntu: `sudo apt-get install libgsl-dev`
+- Arch: `sudo pacman -S gsl`
+- OSX: `brew install gsl` 
+
 ### Bioconda
 
 Rust-Bio-Tools is available via [Bioconda](https://bioconda.github.io).

diff --git a/src/bam/anonymize_reads.rs b/src/bam/anonymize_reads.rs
@@ -23,6 +23,7 @@ pub fn anonymize_reads<P: AsRef<Path> + std::fmt::Debug>(
     let mut fasta_reader = fasta::IndexedReader::from_file(&input_ref)?;
     fasta_reader.fetch(&chr, start, end)?;
     let mut reference = Vec::new();
+    reference.resize((end - start) as usize, 0);
     fasta_reader.read(&mut reference)?;
     let mut rng = rand::thread_rng();
     let alphabet = [b'A', b'C', b'G', b'T'];
@@ -58,7 +59,7 @@ pub fn anonymize_reads<P: AsRef<Path> + std::fmt::Debug>(
         {
             record.cache_cigar();
             //Check if mate record end within region
-            let artificial_seq = if record.is_unmapped() {
+            let artificial_seq = if record.is_unmapped() || record.seq_len() == 0 {
                 let mut seq = Vec::new();
                 add_random_bases(record.seq_len() as u64, &mut seq, &mut rng, &alphabet)?;
                 seq
@@ -98,22 +99,17 @@ fn init_altered_bases(
 
 fn build_record(record: &bam::Record, artificial_seq: &[u8], offset: i64) -> Result<bam::Record> {
     let mut artificial_record = bam::record::Record::new();
-    if let Ok(mate_cigar) = record.aux(b"MC") {
-        artificial_record.push_aux(b"MC", mate_cigar)?;
-    }
     artificial_record.set(
         record.qname(),
         Some(&record.cigar()),
         artificial_seq,
         record.qual(),
     );
-    artificial_record.set_pos(record.pos() - offset);
-    artificial_record.set_tid(0);
-    artificial_record.set_mtid(0);
-    artificial_record.set_mpos(record.mpos() - offset);
-    artificial_record.set_flags(record.flags());
-    artificial_record.set_insert_size(record.insert_size());
-    artificial_record.set_mapq(record.mapq());
+    set_mandatory_fields(&mut artificial_record, record, offset)?;
+    for aux_result in record.aux_iter() {
+        let (tag, aux_field) = aux_result?;
+        artificial_record.push_aux(tag, aux_field)?;
+    }
     Ok(artificial_record)
 }
 
@@ -169,6 +165,28 @@ fn build_sequence(
     Ok(artificial_seq)
 }
 
+fn set_mandatory_fields(
+    target_rec: &mut bam::Record,
+    source_rec: &bam::Record,
+    offset: i64,
+) -> Result<()> {
+    target_rec.set_pos(source_rec.pos() - offset);
+    target_rec.set_tid(0);
+    let (mtid, mpos) = if source_rec.mtid() == -1 {
+        (-1, -1)
+    } else if source_rec.mtid() == source_rec.tid() {
+        (0, source_rec.mpos() - offset)
+    } else {
+        (1, source_rec.mpos())
+    };
+    target_rec.set_mtid(mtid);
+    target_rec.set_mpos(mpos);
+    target_rec.set_flags(source_rec.flags());
+    target_rec.set_insert_size(source_rec.insert_size());
+    target_rec.set_mapq(source_rec.mapq());
+    Ok(())
+}
+
 fn add_random_bases(
     length: u64,
     seq: &mut Vec<u8>,