Update v0.10.0

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "nanoq"
-version = "0.9.0"
+version = "0.10.0"
 authors = ["esteinig <eike.steinig@unimelb.edu.au>", "ljmcoin <lachlan.coin@unimelb.edu.au>"]
 description = "Minimal but speedy quality control and summaries of nanopore reads"
 documentation = "https://github.com/esteinig/nanoq"

Dockerfile

@@ -1,6 +1,6 @@
 FROM alpine:latest
 
-ENV VERSION=0.9.0
+ENV VERSION=0.10.0
 ENV RELEASE=nanoq-${VERSION}-x86_64-unknown-linux-musl.tar.gz
 
 RUN apk update && apk add --no-cache wget

README.md

@@ -2,14 +2,14 @@
 
 [![build](https://github.com/esteinig/nanoq/actions/workflows/rust-ci.yaml/badge.svg?branch=master)](https://github.com/esteinig/nanoq/actions/workflows/rust-ci.yaml)
 [![codecov](https://codecov.io/gh/esteinig/nanoq/branch/master/graph/badge.svg?token=1X04YD8YOE)](https://codecov.io/gh/esteinig/nanoq)
-![](https://img.shields.io/badge/version-0.9.0-black.svg)
+![](https://img.shields.io/badge/version-0.10.0-black.svg)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02991/status.svg)](https://doi.org/10.21105/joss.02991)
 
 Ultra-fast quality control and summary reports for nanopore reads
 
 ## Overview
 
-**`v0.9.0`**
+**`v0.10.0`**
 
 - [Purpose](#purpose)
 - [Install](#install)
@@ -38,7 +38,7 @@ We would appreciate a citation if you are using `nanoq` for research. Please see
 
 ## Performance
 
-`Nanoq` is as fast as `seqtk-fqchk` for summary statistics of small datasets (e.g. Zymo - 100,000 reads) and slightly faster on large datasets (e.g. Zymo - 3.5 million reads, 1.3x - 1.5x). In `fast` mode (no quality scores), `nanoq` is (~2-3x) faster than `rust-bio-tools` and `seqkit stats` for summary statistics and faster than other commonly used summary reporters (up to 442x) and read filtering methods (up to 297x). Memory consumption is consistent and tends to be lower than other tools (~5-10x). 
+`Nanoq` is as fast as `seqtk-fqchk` for summary statistics of small datasets (e.g. Zymo - 100,000 reads) and slightly faster on large datasets (e.g. Zymo - 3.5 million reads, 1.3x - 1.5x). In `fast` mode (no quality scores), `nanoq` is ~2-3x faster than `rust-bio-tools` and `seqkit stats` for summary statistics and other commonly used read summary or filtering methods (up to 297x-442x). Memory consumption is consistent and tends to be lower than other tools (~5-10x). 
 
 ## Tests
 
@@ -61,15 +61,15 @@ cargo install nanoq
 Explicit version (for some reason defaults to old version)
 
 ```
-conda install -c conda-forge -c bioconda nanoq=0.9.0
+conda install -c conda-forge -c bioconda nanoq=0.10.0
 ```
 
 #### `Binaries`
 
 Precompiled binaries for Linux and MacOS are attached to the latest release.
 
 ```
-VERSION=0.9.0
+VERSION=0.10.0
 RELEASE=nanoq-${VERSION}-x86_64-unknown-linux-musl.tar.gz
 
 wget https://github.com/esteinig/nanoq/releases/download/${VERSION}/${RELEASE}
@@ -95,6 +95,14 @@ Reads can be filtered by minimum read length (`-l`), maximum read length (`-m`),
 nanoq -i test.fq -l 1000 -m 10000 -q 10 -w 15 > reads.fq 
 ```
 
+### Read trimming
+
+A fixed number of bases can be trimmed from the start (`-S`) or end (`-E`) of reads:
+
+```bash
+nanoq -i test.fq -S 100 -E 100 > reads.fq 
+```
+
 ### Read report
 
 Read summaries are produced when using the stats flag (`-s`, report to `stdout`, no read output to `stdout`) or when specifying a report file (`-r`):
@@ -147,9 +155,9 @@ done
 ### Parameters
 
 ```
-nanoq 0.9.0
+nanoq 0.10.0
 
-Read filters and summary reports for nanopore data
+Filters and summary reports for nanopore reads
 
 USAGE:
     nanoq [FLAGS] [OPTIONS]
@@ -172,12 +180,26 @@ OPTIONS:
     -q, --min-qual <FLOAT>         Minimum average read quality filter (Q) [default: 0]
     -o, --output <output>          Output filepath, stdout if not present
     -O, --output-type <u|b|g|l>    u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
-    -r, --report <report>          Summary read statistics report output file
+    -r, --report <FILE>            Summary read statistics report output file
     -t, --top <INT>                Number of top reads in verbose summary [default: 5]
+    -L, --read-lengths <FILE>      Output read lengths of surviving reads to file
+    -Q, --read-qualities <FILE>    Output read qualities of surviving reads to file
+    -S, --trim-start <INT>         Trim bases from the start of each read [default: 0]
+    -E, --trim-end <INT>           Trim bases from the end of each read [default: 0]
 ```
 
 ### Output
 
+#### Read lengths and qualities
+
+Files with read lengths (`--read-lengths/-L`) and qualities (`--read-qualities/-Q`) of the surviving reads can be output:
+
+```
+nanoq -i test.fq -Q rq.txt -L rl.txt > reads.fq
+```
+
+#### Summary reports
+
 Summary reports are output to file explicitly using `--report/-r`:
 
 ```bash