update to v1.6.0

huishenlab · Dec 16, 2024 · 6bd14c5 · 6bd14c5
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diff --git 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
@@ -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
@@ -12,7 +12,7 @@ Usage: biscuit vcf2bed [options] <in.vcf>
 
 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
@@ -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
@@ -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 <[email protected]>
 
 Usage: biscuit <command> [options]