update README and Dockerfile to v1.0.5

Cargo.lock

@@ -65,7 +65,7 @@ dependencies = [
 
 [[package]]
 name = "bamcalib"
-version = "0.1.4"
+version = "0.1.5"
 dependencies = [
  "bam",
  "bigtools",

Dockerfile

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: AGPL-3.0-or-later
 FROM rust:1.67-alpine3.17 AS build
 
-RUN apk add --no-cache musl-dev pkgconfig openssl-dev && cargo install bamcalib --version 0.1.3
+RUN apk add --no-cache musl-dev pkgconfig openssl-dev && cargo install bamcalib --version 0.1.5
 
 FROM alpine:3.17
 

README.md

@@ -20,13 +20,13 @@ You need `cargo` installed
 Then run the following command:
 
 ```sh
-cargo install bamcalib --version 0.1.4
+cargo install bamcalib --version 0.1.5
 ```
 
-You can also use the `lbmc/bamcalib:0.1.4` Docker image
+You can also use the `lbmc/bamcalib:0.1.5` Docker image
 
 ```sh
-docker run -it lbmc/bamcalib:0.1.4 bamcalib
+docker run -it lbmc/bamcalib:0.1.5 bamcalib
 ```
 
 ## Usage
@@ -59,6 +59,8 @@ The `bamcalib` expect the following parameters:
   - not passing quality controls
   - PCR or optical duplicate
 - `-t`, `--thread <thread>`            number of threads to parse bam files and write the bigwig file
+- `--no-fragment-estimation`   compute coverage from read information instead of fragment estimation
+- `--intermediate-bigwig`      output normIP and normWCE bigwig files (not just the ratio of the two)
 - `-V`, `--version`                    Print version information
 
 ## Method