rename fqcv to stitch

fulcrumgenomics · Sep 13, 2023 · 7e5c552 · 7e5c552
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diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,11 +1,12 @@
 [workspace]
-members = ["fqcv-lib", "fqcv-cli"]
+members = ["fg-stitch-lib", "fg-stitch-cli"]
+resolver = "2"
 
 [workspace.package]
 authors = ["Fulcrum Genomics LLC"]
 edition = "2021"
 license = "MIT"
-repository = "https://github.com/fulcrumgenomics/fqcv"
+repository = "https://github.com/fulcrumgenomics/fg-stitch"
 version = "0.1.0"
 
 [workspace.dependencies]

diff --git a/README.md b/README.md
@@ -1,36 +1,37 @@
-# fqcv
+# stitch
 
 <p align="center">
-  <a href="https://github.com/fulcrumgenomics/fqcv/actions?query=workflow%3ACheck"><img src="https://github.com/fulcrumgenomics/fqcv/actions/workflows/build_and_test.yml/badge.svg" alt="Build Status"></a>
+  <a href="https://github.com/fulcrumgenomics/stitch/actions?query=workflow%3ACheck"><img src="https://github.com/fulcrumgenomics/stitch/actions/workflows/build_and_test.yml/badge.svg" alt="Build Status"></a>
   <br>
 </p>
 
 Alignment for vector quality control
 
 <!---toc start-->
-* [fqcv align](#fqcv-align)
-  * [Optional Pre-alignment](#optional-pre-alignment)
-  * [Alignment Scoring](#alignment-scoring)
-  * [Alignment mode](#alignment-mode)
-  * [Circular contigs](#circular-contigs)
-  * [Additional Output Options](#additional-output-options)
-* [Installing](#installing)
-  * [Installing with cargo](#installing-with-cargo)
-  * [Building From Source](#building-from-source)
-* [Developing](#developing)
-* [Releasing a New Version](#releasing-a-new-version)
-  * [Pre-requisites](#pre-requisites)
-  * [Prior to Any Release](#prior-to-any-release)
-  * [Semantic Versioning](#semantic-versioning)
-  * [Major Release](#major-release)
-  * [Minor and Patch Release](#minor-and-patch-release)
-  * [Release Candidate](#release-candidate)
+- [stitch](#stitch)
+  - [stitch align](#stitch-align)
+    - [Optional Pre-alignment](#optional-pre-alignment)
+    - [Alignment Scoring](#alignment-scoring)
+    - [Alignment mode](#alignment-mode)
+    - [Circular contigs](#circular-contigs)
+    - [Additional Output Options](#additional-output-options)
+  - [Installing](#installing)
+    - [Installing with `cargo`](#installing-with-cargo)
+    - [Building From Source](#building-from-source)
+  - [Developing](#developing)
+  - [Releasing a New Version](#releasing-a-new-version)
+    - [Pre-requisites](#pre-requisites)
+    - [Prior to Any Release](#prior-to-any-release)
+    - [Semantic Versioning](#semantic-versioning)
+    - [Major Release](#major-release)
+    - [Minor and Patch Release](#minor-and-patch-release)
+    - [Release Candidate](#release-candidate)
 
 <!---toc end-->
 
-## fqcv align
+## stitch align
 
-Perfoms alignment of a long reads against one or more reference/expected vector/plasmid/construct(s).
+Perfoms alignment of long reads against one or more reference/expected vector/plasmid/construct(s).
 
 The alignment extends the traditional alignment algorithms by introducing a "jump" move/operator, 
 whereby the alignment is able to jump anywhere in the reference sequence for a fixed cost.  This 
@@ -104,18 +105,18 @@ Which (On Mac OS and Linux) can be done with the command:
 curl https://sh.rustup.rs -sSf | sh
 ```
 
-Then, to install `fqcv` run:
+Then, to install `stitch` run:
 
 ```console
-cargo install fqcv
+cargo install fg-stitch
 ```
 
 ### Building From Source
 
 First, clone the git repo:
 
 ```console
-git clone https://github.com/fulcrumgenomics/fqcv.git
+git clone https://github.com/fulcrumgenomics/stitch.git
 ```
 
 Secondly, if you do not already have rust development tools installed, install via [rustup](https://rustup.rs/):
@@ -127,15 +128,15 @@ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
 Then build the toolkit in release mode:
 
 ```console
-cd fqcv
+cd stitch
 cargo build --release
-./target/release/fqcv --help
+./target/release/stitch --help
 ```
 
 ## Developing
 
-fqcv is developed in Rust and follows the conventions of using `rustfmt` and `clippy` to ensure both code quality and standardized formatting.
-When working on fqcv, before pushing any commits, please first run `./ci/check.sh` and resolve any issues that are reported.
+`stitch` is developed in Rust and follows the conventions of using `rustfmt` and `clippy` to ensure both code quality and standardized formatting.
+When working on `stitch`, before pushing any commits, please first run `./ci/check.sh` and resolve any issues that are reported.
 
 ## Releasing a New Version
 
@@ -203,4 +204,4 @@ If you would like to tag the release candidate on github, remove `--no-tag` to c
 
 [cargo-release-link]:      https://github.com/crate-ci/cargo-release
 [cargo-release-docs-link]: https://github.com/crate-ci/cargo-release/blob/master/docs/reference.md
-[new-release-link]:        https://github.com/fulcrumgenomics/fqcv/releases/new
+[new-release-link]:        https://github.com/fulcrumgenomics/stitch/releases/new
diff --git a/fqcv-cli/Cargo.toml → fg-stitch-cli/Cargo.toml b/fqcv-cli/Cargo.toml → fg-stitch-cli/Cargo.toml
@@ -1,14 +1,14 @@
 [package]
-name = "fqcv"
-description = "FQCV is an aligner for long reads against one or more reference/expected vector/plasmid/construct(s)."
+name = "fg-stitch"
+description = "Stitch is an aligner for long reads against one or more reference/expected vector/plasmid/construct(s)."
 authors.workspace = true
 edition.workspace = true
 license.workspace = true
 repository.workspace = true
 version.workspace = true
 
 [[bin]]
-name = "fqcv"
+name = "stitch"
 path = "src/main.rs"
 
 [dependencies]
@@ -17,7 +17,7 @@ clap = { version = "4.2.7", features = ["derive", "string"] }
 enum_dispatch = "0.3.12"
 env_logger = "0.10.0"
 flume.workspace = true
-fqcv-lib = { version = "0.1.0", path = "../fqcv-lib" }
+stitch = { version = "0.1.0", path = "../fg-stitch-lib", package = "fg-stitch-lib" }
 itertools.workspace = true
 log = "0.4.17"
 noodles.workspace = true

diff --git a/fqcv-cli/src/commands/align.rs → fg-stitch-cli/src/commands/align.rs b/fqcv-cli/src/commands/align.rs → fg-stitch-cli/src/commands/align.rs
@@ -5,19 +5,6 @@ use clap::{
     Parser,
 };
 use flume::unbounded;
-use fqcv_lib::{
-    align::{
-        io::{
-            FastqGroupingIterator, FastqThreadReader, OutputMessage, OutputResult,
-            READER_CHANNEL_NUM_CHUNKS,
-        },
-        AlignmentMode, Builder, PrimaryPickingStrategy,
-    },
-    util::{
-        target_seq,
-        version::{built_info, built_info::VERSION},
-    },
-};
 use itertools::{self, Itertools};
 use log::info;
 use noodles::{
@@ -37,6 +24,19 @@ use std::{
     env, io, io::Write, num::NonZeroUsize, path::PathBuf, sync::Arc, thread::JoinHandle,
     time::Duration,
 };
+use stitch::{
+    align::{
+        io::{
+            FastqGroupingIterator, FastqThreadReader, OutputMessage, OutputResult,
+            READER_CHANNEL_NUM_CHUNKS,
+        },
+        AlignmentMode, Builder, PrimaryPickingStrategy,
+    },
+    util::{
+        target_seq,
+        version::{built_info, built_info::VERSION},
+    },
+};
 
 ////////////////////////////////////////////////////////////////////////////////
 // Align (main class) and it's impls
@@ -277,7 +277,7 @@ impl Align {
         info!("Reading reads FASTQ from {}", self.reads_fastq.display());
         // ensure!(self. > 1, "Must specify at least two threads");
         let progress_logger = ProgLogBuilder::new()
-            .name("fqcv-progress")
+            .name("stitch-progress")
             .noun("reads")
             .verb("Processed")
             .unit(
@@ -388,9 +388,9 @@ impl Align {
         let mut writer = BamWriter::from(encoder);
         let header = {
             let mut builder = SamHeader::builder().set_header(Map::default()).add_program(
-                "fqcv",
+                "stitch",
                 Map::<Program>::builder()
-                    .set_name("fqcv")
+                    .set_name("stitch")
                     .set_version(VERSION.clone())
                     .set_command_line(command_line)
                     .build()?,

diff --git a/fqcv-cli/src/commands/command.rs → fg-stitch-cli/src/commands/command.rs b/fqcv-cli/src/commands/command.rs → fg-stitch-cli/src/commands/command.rs
diff --git a/fqcv-cli/src/commands/mod.rs → fg-stitch-cli/src/commands/mod.rs b/fqcv-cli/src/commands/mod.rs → fg-stitch-cli/src/commands/mod.rs
diff --git a/fqcv-cli/src/main.rs → fg-stitch-cli/src/main.rs b/fqcv-cli/src/main.rs → fg-stitch-cli/src/main.rs
@@ -1,11 +1,11 @@
-pub mod commands;
+mod commands;
 
 use anyhow::Result;
 use clap::Parser;
 use commands::{align::Align, command::Command};
 use enum_dispatch::enum_dispatch;
 use env_logger::Env;
-use fqcv_lib::util::version::built_info;
+use stitch::util::version::built_info;
 
 // #[global_allocator]
 // static GLOBAL: mimalloc::MiMalloc = mimalloc::MiMalloc;

diff --git a/fqcv-lib/Cargo.toml → fg-stitch-lib/Cargo.toml b/fqcv-lib/Cargo.toml → fg-stitch-lib/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
-name = "fqcv-lib"
-description = "FQCV aligner implementation and supporting utilities."
+name = "fg-stitch-lib"
+description = "Stitch aligner implementation and supporting utilities."
 authors.workspace = true
 edition.workspace = true
 license.workspace = true

diff --git a/fqcv-lib/build.rs → fg-stitch-lib/build.rs b/fqcv-lib/build.rs → fg-stitch-lib/build.rs
diff --git a/fqcv-lib/src/align/aligners/constants.rs → ...titch-lib/src/align/aligners/constants.rs b/fqcv-lib/src/align/aligners/constants.rs → ...titch-lib/src/align/aligners/constants.rs
diff --git a/fqcv-lib/src/align/aligners/mod.rs → fg-stitch-lib/src/align/aligners/mod.rs b/fqcv-lib/src/align/aligners/mod.rs → fg-stitch-lib/src/align/aligners/mod.rs
diff --git a/...rc/align/aligners/multi_contig_aligner.rs → ...rc/align/aligners/multi_contig_aligner.rs b/...rc/align/aligners/multi_contig_aligner.rs → ...rc/align/aligners/multi_contig_aligner.rs
diff --git a/...c/align/aligners/single_contig_aligner.rs → ...c/align/aligners/single_contig_aligner.rs b/...c/align/aligners/single_contig_aligner.rs → ...c/align/aligners/single_contig_aligner.rs
diff --git a/fqcv-lib/src/align/alignment.rs → fg-stitch-lib/src/align/alignment.rs b/fqcv-lib/src/align/alignment.rs → fg-stitch-lib/src/align/alignment.rs
diff --git a/fqcv-lib/src/align/io.rs → fg-stitch-lib/src/align/io.rs b/fqcv-lib/src/align/io.rs → fg-stitch-lib/src/align/io.rs
diff --git a/fqcv-lib/src/align/mod.rs → fg-stitch-lib/src/align/mod.rs b/fqcv-lib/src/align/mod.rs → fg-stitch-lib/src/align/mod.rs
diff --git a/fqcv-lib/src/align/scoring.rs → fg-stitch-lib/src/align/scoring.rs b/fqcv-lib/src/align/scoring.rs → fg-stitch-lib/src/align/scoring.rs
diff --git a/fqcv-lib/src/align/sub_alignment.rs → fg-stitch-lib/src/align/sub_alignment.rs b/fqcv-lib/src/align/sub_alignment.rs → fg-stitch-lib/src/align/sub_alignment.rs
diff --git a/fqcv-lib/src/align/traceback/mod.rs → fg-stitch-lib/src/align/traceback/mod.rs b/fqcv-lib/src/align/traceback/mod.rs → fg-stitch-lib/src/align/traceback/mod.rs
diff --git a/...src/align/traceback/packed_length_cell.rs → ...src/align/traceback/packed_length_cell.rs b/...src/align/traceback/packed_length_cell.rs → ...src/align/traceback/packed_length_cell.rs
diff --git a/fqcv-lib/src/align/traceback/simple_cell.rs → ...ch-lib/src/align/traceback/simple_cell.rs b/fqcv-lib/src/align/traceback/simple_cell.rs → ...ch-lib/src/align/traceback/simple_cell.rs
diff --git a/fqcv-lib/src/lib.rs → fg-stitch-lib/src/lib.rs b/fqcv-lib/src/lib.rs → fg-stitch-lib/src/lib.rs
diff --git a/fqcv-lib/src/util/dna.rs → fg-stitch-lib/src/util/dna.rs b/fqcv-lib/src/util/dna.rs → fg-stitch-lib/src/util/dna.rs
diff --git a/fqcv-lib/src/util/index_map.rs → fg-stitch-lib/src/util/index_map.rs b/fqcv-lib/src/util/index_map.rs → fg-stitch-lib/src/util/index_map.rs
diff --git a/fqcv-lib/src/util/io.rs → fg-stitch-lib/src/util/io.rs b/fqcv-lib/src/util/io.rs → fg-stitch-lib/src/util/io.rs
diff --git a/fqcv-lib/src/util/mod.rs → fg-stitch-lib/src/util/mod.rs b/fqcv-lib/src/util/mod.rs → fg-stitch-lib/src/util/mod.rs
diff --git a/fqcv-lib/src/util/target_seq.rs → fg-stitch-lib/src/util/target_seq.rs b/fqcv-lib/src/util/target_seq.rs → fg-stitch-lib/src/util/target_seq.rs
diff --git a/fqcv-lib/src/util/version.rs → fg-stitch-lib/src/util/version.rs b/fqcv-lib/src/util/version.rs → fg-stitch-lib/src/util/version.rs