diff --git a/docs/releases.md b/docs/releases.md index 5a1a6c5..9d94d44 100644 --- a/docs/releases.md +++ b/docs/releases.md @@ -12,8 +12,12 @@ details regarding each release, see the "Find it on GitHub" link under each rele **Note, releases starting at version 1.0.0 are not backwards compatible with version 0.3.16 and earlier.** - - **Version 1.5.0** + - **Version 1.6.0** - *Latest Release* + - Released: 16 December 2024 + - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.6.0.20241216) + + - **Version 1.5.0** - Released: 6 May 2024 - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.5.0.20240506) diff --git a/docs/subcommands/biscuit_bsconv.md b/docs/subcommands/biscuit_bsconv.md index 7554aae..397f66e 100644 --- a/docs/subcommands/biscuit_bsconv.md +++ b/docs/subcommands/biscuit_bsconv.md @@ -19,6 +19,7 @@ Options: -a INT Filter: maximum CpA retention [Inf] -c INT Filter: maximum CpC retention [Inf] -t INT Filter: maximum CpT retention [Inf] + -x INT Filter: maximum CpY retention [Inf] -p Print in tab-separated format, print order: CpA_R, CpA_C, CpC_R, CpC_C, CpG_R, CpG_C, CpT_R, CpT_C -v Show filtered reads instead of remaining reads diff --git a/docs/subcommands/biscuit_vcf2bed.md b/docs/subcommands/biscuit_vcf2bed.md index 19f8d62..8806a4a 100644 --- a/docs/subcommands/biscuit_vcf2bed.md +++ b/docs/subcommands/biscuit_vcf2bed.md @@ -12,7 +12,7 @@ Usage: biscuit vcf2bed [options] Options: -t STR Extract type {c, cg, ch, hcg, gch, snp} [CG] - -k INT Minimum coverage [3] + -k INT Minimum coverage (see Note 1) [1] -s STR Sample, (takes "FIRST", "LAST", "ALL", or specific sample names separated by ",") [FIRST] -e Show context (reference base, context group {CG,CHG,CHH}, @@ -21,4 +21,8 @@ Options: -c Output Beta-M-U instead of Beta-Cov. -h This help +Note 1: Starting with version 1.6.0, the default minimum coverage was changed from + three (3) to one (1) to better match other tools and serve as a better default + for single-cell experiments. + ``` diff --git a/docs/subcommands/biscuit_version.md b/docs/subcommands/biscuit_version.md index c32cf6b..b974dad 100644 --- a/docs/subcommands/biscuit_version.md +++ b/docs/subcommands/biscuit_version.md @@ -7,11 +7,12 @@ permalink: /biscuit_version/ # biscuit version ```bash -BISCUIT Version: 1.5.0 +BISCUIT Version: 1.6.0 Using: htslib : version 1.18 sgsl : huishenlab/sgsl at commit 6533277 utils : huishenlab/utils at commit 5f4aeab +Libraries found at: https://github.com/huishenlab/biscuit/tree/master/lib ``` diff --git a/docs/subcommands/subcommand_help.md b/docs/subcommands/subcommand_help.md index 47319e7..9939b7c 100644 --- a/docs/subcommands/subcommand_help.md +++ b/docs/subcommands/subcommand_help.md @@ -12,7 +12,7 @@ Usage for all BISCUIT subcommands as of BISCUIT version 1.4.0 (printed with eith ```bash Program: BISCUIT (BISulfite-seq CUI Toolkit) -Version: 1.5.0 +Version: 1.6.0 Contact: Jacob Morrison Usage: biscuit [options]