fix version issues

README.md

@@ -1,10 +1,10 @@
 <img alt="logo" src="https://github.com/COMBINE-lab/alevin-fry/raw/master/docs/logo.png" width="200">
 
-# alevin-fry ![Rust](https://github.com/COMBINE-lab/alevin-fry/workflows/Rust/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/platforms.svg)](https://anaconda.org/bioconda/alevin-fry) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/license.svg)](https://anaconda.org/bioconda/alevin-fry)
+# alevin-fry ![Rust](https://github.com/COMBINE-lab/alevin-fry/workflows/Rust/badge.svg) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/platforms.svg)](https://anaconda.org/bioconda/alevin-fry) [![Anaconda-Server Badge](https://anaconda.org/bioconda/alevin-fry/badges/license.svg)](https://anaconda.org/bioconda/alevin-fry) ![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/combine-lab/alevin-fry?style=flat-square)
 
 `alevin-fry` is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data.  It consumes RAD files generated by `salmon alevin`, and performs common operations like generating permit lists, and estimating the number of distinct molecules from each gene within each cell.  The focus in `alevin-fry` is on safety, accuracy and efficiency (in terms of both time and memory usage).
 
-You can read the pre-print describing alevin-fry : ["Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data"](https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1) on bioRxiv.
+You can read the paper describing alevin fry, "Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data" [here](https://www.nature.com/articles/s41592-022-01408-3), and the pre-print [on bioRxiv](https://www.biorxiv.org/content/10.1101/2021.06.29.450377v1).
 
 * [**Quickstart guide with a unified singularity container**](https://github.com/COMBINE-lab/alevin-fry#a-quick-start-run-through-on-sample-data)
 
@@ -24,6 +24,8 @@ The generation of the reduced alignment data (RAD) files processed by alevin-fry
 
 The [`usefulaf`](https://github.com/COMBINE-lab/usefulaf) repository contains scripts in functions that are useful in helping to prepare input for alevin-fry processing, importing alevin-fry output into downstream analysis evnironemnts, and even [running common configurations of alevin-fry more simply](https://github.com/COMBINE-lab/usefulaf/blob/main/bash/simpleaf.sh).  This repository also contains the relevant [Python function](https://github.com/COMBINE-lab/usefulaf/blob/main/python/load_fry.py) for loading fry output (specifically in USA mode) in a convenient way into [scanpy](https://scanpy.readthedocs.io/en/stable/) (i.e. as [AnnData](https://scanpy.readthedocs.io/en/latest/usage-principles.html#anndata) objects) for subsequent Python-based processing in scanpy.
 
+The [`roe`](https://github.com/COMBINE-lab/roe) and [`pyroe`](https://github.com/COMBINE-lab/pyroe) repositories provide tools to help easily construct a _splici_ transcriptome from a reference genome and GTF file in `R` and `python` respectively.
+
 The [`fishpond`](https://github.com/mikelove/fishpond) package — maintained by @mikelove and his lab — contains the recommended relevant functions for reading `alevin-fry` output (particularly USA-mode output) into the R ecosystem, in the form of a [`singleCellExperiment`](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) object.
 
 The [`alevinqc`](https://github.com/csoneson/alevinQC) package — maintained by @csoneson — provides tool and functions for performing quality control and assessment downstream of `alevin-fry`.
@@ -100,6 +102,7 @@ Finally, we'll download the [singularity](https://sylabs.io/singularity/) image
 ```{bash}
 $ wget -v -O usefulaf.sif https://umd.box.com/shared/static/bcd8io9fbjc321pfgcomues5oe2a12cz
 ```
+
 or, alternatively, you can pull the docker image directly from Dockerhub and have singularity convert it for you
 
 ```{bash}
@@ -108,7 +111,7 @@ $ singularity pull docker://combinelab/usefulaf:latest
 
 ### Info about the singularity container
 
-The singularity container we just downloaded above contains a recent release of `salmon` (v1.5.1) and `alevin-fry` (v0.4.0), as well as an installation of `R` and all of the packages needed to build the _splici_ index.
+The singularity container we just downloaded above contains a recent release of `salmon` (v1.8.0) and `alevin-fry` (v0.5.0), as well as an installation of `R` and all of the packages needed to build the _splici_ index.
 
 To build the reference index (and quantify) we'll use the [simpleaf](https://github.com/COMBINE-lab/usefulaf/blob/main/bash/simpleaf) wrapper.  This is a shell script written around `salmon`, `alevin-fry`, and the _splici_ index construction code that simplifies processing by grouping together related commands, using a fixed directory structure for processing, and also by eliminating some different options that are otherwise exposed by `salmon` and `alevin-fry` (e.g. it builds the `sparse` index, maps in `sketch` mode etc.).  If you would like to run the "raw" commands, the Singularity image contains `salmon` and `alevin-fry` in the path, and the `R` script to construct the _splici_ index at `/usefulaf/R/build_splici_ref.R`, so you can explore more detailed options.
 
@@ -199,4 +202,29 @@ that you should pass to `alevin-fry` during the `quant` phase.
 If you have any questions about preparing the splici reference, or otherwise about processing your data with `alevin-fry` please feel free to open an issue 
 here on GitHub!
 
+## Citing alevin-fry
+
+If you use `alevin-fry` in your work, please cite:
+
+```
+He, D., Zakeri, M., Sarkar, H. et al. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022). https://doi.org/10.1038/s41592-022-01408-3
+```
+
+**BibTeX:**
+```
+@Article{He2022,
+author={He, Dongze and Zakeri, Mohsen and Sarkar, Hirak and Soneson, Charlotte and Srivastava, Avi and Patro, Rob},
+title={Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data},
+journal={Nature Methods},
+year={2022},
+month={Mar},
+day={01},
+volume={19},
+number={3},
+pages={316-322},
+issn={1548-7105},
+doi={10.1038/s41592-022-01408-3},
+url={https://doi.org/10.1038/s41592-022-01408-3}
+}
+```
 

src/main.rs

@@ -7,14 +7,14 @@
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
 
-extern crate bio_types;
-extern crate chrono;
-extern crate clap;
-extern crate itertools;
-extern crate num_cpus;
-extern crate rand;
-extern crate slog;
-extern crate slog_term;
+
+use chrono;
+
+
+use num_cpus;
+use rand;
+use slog;
+use slog_term;
 
 use bio_types::strand::Strand;
 use clap::{arg, crate_authors, crate_version, Command};

src/quant.rs

@@ -72,7 +72,7 @@ pub enum ResolutionStrategy {
 }
 
 impl fmt::Display for ResolutionStrategy {
-    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
         write!(f, "{:?}", self)
     }
 }

src/utils.rs

@@ -745,7 +745,7 @@ impl InternalVersionInfo {
 }
 
 impl fmt::Display for InternalVersionInfo {
-    fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
         write!(f, "v{}.{}.{}", self.major, self.minor, self.patch)
     }
 }