update: prepping update, update manual and help printing

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+- package-ecosystem: cargo
+  directory: "/"
+  schedule:
+    interval: monthly
+    time: "19:00"
+  open-pull-requests-limit: 10
+  ignore:
+  - dependency-name: rust-htslib
+    versions:
+    - 0.36.0
+  - dependency-name: rand
+    versions:
+    - 0.8.0

.github/workflows/release-lorikeet.yml

@@ -7,7 +7,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@main
         if: github.actor != 'dependabot[bot]'
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 
 name = "lorikeet-genome"
-version = "0.7.2"
+version = "0.7.3"
 authors = ["Rhys Newell <rhys.newell@hdr.qut.edu.au>"]
 license = "GPL-3.0"
 description = "Strain resolver and variant caller via local reassembly for metagenomics"
@@ -23,69 +23,59 @@ vendored-openssl = ["openssl-sys/vendored"]
 [dependencies]
 approx = "0.5.0"
 ansi_term = "0.12.1"
-bio = "0.38"
-bio-types = "0.13"
-bird_tool_utils = "^0.3"
+bio = "0.41.0"
+bio-types = "0.13.0"
+bird_tool_utils = { git = "https://github.com/wwood/bird_tool_utils" }
+bird_tool_utils-man = "^0.4"
 bstr = "^0.2.17"
-clap = "2"
+clap = { version="^3", features = ["cargo"] } # cargo feature required for crate_version!
+clap_complete = "^3"
 compare = "0.1.0"
-coverm = {git = "https://github.com/rhysnewell/CoverM"}
-criterion = "0.3.5"
-galah = "^0.3"
-hashlink = "0.7.0"
-csv = "1"
-derive_builder = "0.9"
-derive-new = "0.5"
-debruijn = "0.3.2"
+coverm = {git = "https://github.com/rhysnewell/CoverM", branch = "main"}
+galah = { git = "https://github.com/wwood/galah" }
+hashlink = "^0.7"
+enum-ordinalize = "^3.1"
 env_logger = "0.6"
-enum-ordinalize = "3.1.10"
 glob = "^0.3"
 gkl = "^0.1.1"
-indexmap = "1.7.0"
-itertools = "0.8"
-lazy_static = "1.3.0"
-log = "0.4"
+indexmap = "^1.7"
+itertools = "^0.8"
+lazy_static = "^1.3"
+log = "^0.4"
 libm = "0.2.1"
 mathru = "0.9.1"
 multimap = "0.8.3"
 ndarray-npy = "^0.8.0"
 ndarray = {version = "^0.15.3", features = ["rayon"]}
 needletail = "^0.4.1"
-nix = "0.24"
-ntest = "0.7.3"
 num = "0.4.0"
 openssl-sys = "0.9"
 openssl = "0.10"
 ordered-float = "1"
-pest = "2"
-pest_derive = "2"
 petgraph = {version = "^0.6.0", features = ["stable_graph"]}
-#polars = "0.22.8"
 pyo3 = "^0.16.5"
 rand = "0.6"
 rayon = "^1.5.1"
-rust-htslib = "0.38.2"
-seq_io = "^0.3"
+roff = "^0.2"
+rust-htslib = { version="0.39.*", default-features = false }
+serde = "^1"
+serde_derive = "^1"
 strum = "^0.17.1"
 strum_macros = "^0.17.1"
-serde = "1"
-serde_derive = "1"
-serde_json = "1"
-serde_yaml = "0.8"
 statrs = "0.13"
-tempdir = "0.3"
-tempfile = "3.0"
+tempdir = "^0.3"
+tempfile = "^3"
 term = "0.7.0"
-indicatif = "^0.16.0"
+indicatif = "^0.17.1"
 scoped_threadpool = "^0.1.9"
 
 
 [lib]
 bench = false
 
-[[bench]]
-name = "benchmarks"
-harness = false
+#[[bench]]
+#name = "benchmarks"
+#harness = false
 
 [dev-dependencies]
 assert_cli = "0.6.*"
@@ -126,7 +116,8 @@ overflow-checks = true # use overflow checks for integer arithmetic.
 opt-level = 3
 debug = false
 rpath = false
-lto = false
+strip = true
+lto = true
 debug-assertions = false
 codegen-units = 16
 panic = 'unwind'

lorikeet.yml

@@ -13,7 +13,7 @@ dependencies:
   - samtools=1.9
   - starcode
   - bwa-mem2
-  - minimap2>=2.20
+  - minimap2>=2.24
 #  - umap-learn>=0.5
 #  - hdbscan
 #  - matplotlib-base

src/assembly/assembly_region_iterator.rs

@@ -64,7 +64,7 @@ impl<'a> AssemblyRegionIterator<'a> {
         args: &clap::ArgMatches,
     ) {
         // We don't need to check previous region reads as the implementation of fetch we have
-        // should retrieve all reads regardles of if they have been seen before
+        // should retrieve all reads regardless of if they have been seen before
 
         let min_mapq = args.value_of("min-mapq").unwrap().parse::<u8>().unwrap();
         let limiting_interval = IntervalUtils::parse_limiting_interval(args);
@@ -81,7 +81,7 @@ impl<'a> AssemblyRegionIterator<'a> {
                 };
 
                 match read_type {
-                    ReadType::Short => {
+                    ReadType::Short | ReadType::Long => {
                         let mut record = Record::new(); // Empty bam record
                         let mut bam_generated = generate_indexed_named_bam_readers_from_bam_files(
                             vec![&bam_generator],
@@ -109,7 +109,7 @@ impl<'a> AssemblyRegionIterator<'a> {
                             if ReadUtils::read_is_filtered(
                                 &record,
                                 flag_filters,
-                                20,
+                                min_mapq,
                                 read_type,
                                 &Self::DUMMY_LIMITING_INTERVAL,
                             )