From 3d36a0cf7043a6307d5446c0455cd0b04565923c Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sat, 29 Jan 2022 22:28:40 -0600 Subject: [PATCH 1/7] joss paper and badges --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 7876ec9..928b1d2 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,15 @@ bam-readcount ============= +![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) +![latest release](https://img.shields.io/github/v/release/genome/bam-readcount) ![tests](https://github.com/seqfu/bam-readcount/actions/workflows/tests.yml/badge.svg?branch=samtools-1.10) ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) +![Docker Pulls](https://img.shields.io/docker/pulls/mgibio/bam-readcount?style=plastic) +![GitHub](https://img.shields.io/github/license/genome/bam-readcount) +Paper for bam-reacound can be found [here](https://doi.org/10.21105/joss.03722) +Please cite it if you found bam-readcount useful for your research. + `bam-readcount` is a utility that runs on a `BAM` or `CRAM` file and generates low-level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, From 0a2bdc3b868d07488b6d86f9bde9fd571a038233 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sat, 29 Jan 2022 22:33:28 -0600 Subject: [PATCH 2/7] joss badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 928b1d2..813d61c 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ bam-readcount ============= -![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) +[![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) ![latest release](https://img.shields.io/github/v/release/genome/bam-readcount) ![tests](https://github.com/seqfu/bam-readcount/actions/workflows/tests.yml/badge.svg?branch=samtools-1.10) ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) From 4a19c8ffc9c649b3c5cc326f2c1a7fe905dbb54b Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sat, 29 Jan 2022 22:34:18 -0600 Subject: [PATCH 3/7] space --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 813d61c..cda59eb 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ bam-readcount ============= -[![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) +[![DOI](https://joss.theoj.org/papers/10.21105/joss.03722/status.svg)](https://doi.org/10.21105/joss.03722) ![latest release](https://img.shields.io/github/v/release/genome/bam-readcount) ![tests](https://github.com/seqfu/bam-readcount/actions/workflows/tests.yml/badge.svg?branch=samtools-1.10) ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) From e9b68f5ccca129eda99a722b446216a601f52b09 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sat, 29 Jan 2022 22:37:24 -0600 Subject: [PATCH 4/7] add AJA citation --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index cda59eb..779e1a4 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,8 @@ bam-readcount ![Docker Pulls](https://img.shields.io/docker/pulls/mgibio/bam-readcount?style=plastic) ![GitHub](https://img.shields.io/github/license/genome/bam-readcount) Paper for bam-reacound can be found [here](https://doi.org/10.21105/joss.03722) -Please cite it if you found bam-readcount useful for your research. +Please cite it if you found bam-readcount useful for your research. +Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. Journal of Open Source Software, 7(69), 3722, https://doi.org/10.21105/joss.03722 `bam-readcount` is a utility that runs on a `BAM` or `CRAM` file and generates low-level information about From 8a3c35c55d3f3826cfe72a528b01819c62b0e9b7 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sun, 30 Jan 2022 10:15:35 -0600 Subject: [PATCH 5/7] typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 779e1a4..540df89 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ bam-readcount ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) ![Docker Pulls](https://img.shields.io/docker/pulls/mgibio/bam-readcount?style=plastic) ![GitHub](https://img.shields.io/github/license/genome/bam-readcount) -Paper for bam-reacound can be found [here](https://doi.org/10.21105/joss.03722) +Paper for bam-readcount can be found [here](https://doi.org/10.21105/joss.03722) Please cite it if you found bam-readcount useful for your research. Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. Journal of Open Source Software, 7(69), 3722, https://doi.org/10.21105/joss.03722 From 6b50d277ec4dfdce8d49d9e50c991c8219765aaf Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sun, 30 Jan 2022 22:52:10 -0600 Subject: [PATCH 6/7] more edits --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 540df89..c59fde7 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,6 @@ bam-readcount ![coverage](https://coveralls.io/repos/seqfu/bam-readcount/badge.svg?branch=samtools-1.10&service=github) ![Docker Pulls](https://img.shields.io/docker/pulls/mgibio/bam-readcount?style=plastic) ![GitHub](https://img.shields.io/github/license/genome/bam-readcount) -Paper for bam-readcount can be found [here](https://doi.org/10.21105/joss.03722) -Please cite it if you found bam-readcount useful for your research. -Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. Journal of Open Source Software, 7(69), 3722, https://doi.org/10.21105/joss.03722 `bam-readcount` is a utility that runs on a `BAM` or `CRAM` file and generates low-level information about @@ -29,6 +26,10 @@ Contents * [Support](#support) * [Contributing](#contributing) +If you find `bam-readcount` useful in your work, please cite our [paper](https://doi.org/10.21105/joss.03722): + +> Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. _Journal of Open Source Software_, 7(69), 3722. https://doi.org/10.21105/joss.03722 + Installation ------------ From 350ecfcc7325616b45d9e14fe4b1dd93618e9209 Mon Sep 17 00:00:00 2001 From: sridhar0605 Date: Sun, 30 Jan 2022 23:10:54 -0600 Subject: [PATCH 7/7] move block --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c59fde7..ac7b075 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,10 @@ Originally designed to help filter genomic mutation calls, the metrics `bam-read are also useful as input for variant detection tools and for resolving ambiguity between variant callers. +If you find `bam-readcount` useful in your work, please cite our [paper](https://doi.org/10.21105/joss.03722): + +> Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. _Journal of Open Source Software_, 7(69), 3722. https://doi.org/10.21105/joss.03722 + Contents --------- * [Installation](#installation) @@ -26,10 +30,6 @@ Contents * [Support](#support) * [Contributing](#contributing) -If you find `bam-readcount` useful in your work, please cite our [paper](https://doi.org/10.21105/joss.03722): - -> Khanna et al., (2022). Bam-readcount - rapid generation of basepair-resolution sequence metrics. _Journal of Open Source Software_, 7(69), 3722. https://doi.org/10.21105/joss.03722 - Installation ------------