update release and subcommand pages

huishenlab · May 6, 2024 · c2aa114 · c2aa114
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Showing 6 changed files with 14 additions and 7 deletions.
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 1.4.0**
+  - **Version 1.5.0**
     - *Latest Release*
+    - Released: 6 May 2024
+    - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.5.0.20240506)
+
+  - **Version 1.4.0**
     - Released: 8 January 2024
     - [Find it on GitHub](https://github.com/huishenlab/biscuit/releases/tag/v1.4.0.20240108)
 

diff --git a/docs/subcommands/biscuit_align.md b/docs/subcommands/biscuit_align.md
@@ -39,7 +39,7 @@ Algorithm options:
     -S              Skip mate rescue
     -P              Skip pairing - mate rescue performed unless -S also given
     -e              Discard full-length exact matches
-    -9              Extract barcode from read comment
+    -9              Extract barcode and UMI from read name
 
 Scoring options:
     -A INT          Score for a sequence match, scales options -TdBOELU unless

diff --git a/docs/subcommands/biscuit_bc.md b/docs/subcommands/biscuit_bc.md
@@ -19,6 +19,8 @@ Output Options:
 General Options:
     -h, --help             This help
 
-Note: When writing to stdout, reads 1 and 2 will alternate (i.e., are interleaved)
+Note 1: When writing to stdout, reads 1 and 2 will alternate (i.e., are interleaved)
+Note 2: Also adds an artificial UMI (AAAAAAAA) for compatibility purposes and to serve
+        as a placeholder for future UMI work
 
 ```
diff --git a/docs/subcommands/biscuit_epiread.md b/docs/subcommands/biscuit_epiread.md
@@ -19,7 +19,8 @@ Options:
 Output options:
     -o STR    Output file [stdout]
     -N        NOMe-seq mode [off]
-    -L        Data is from long read sequencing [off]
+    -L INT    maximum read length (will need to be increased for long reads) [302]
+    -M        BAM file has modBAM tags (MM/ML) [off]
     -P        Pairwise mode [off]
     -O        Old BISCUIT epiread format, not compatible with -P [off]
     -A        Print all CpG and SNP locations in location column, ignored if -O not given [off]
@@ -39,6 +40,7 @@ Filter options:
     -u        NO filtering of duplicate
     -p        NO filtering of improper pair
     -n INT    Maximum NM tag [999999]
+    -y FLT    Minimum probability a modification is correct (0.0 - 1.0) [0.900000]
     -h        This help
 
 Note, the -O (old epiread format) and -P (pairwise format for biscuit asm) are not guaranteed

diff --git a/docs/subcommands/biscuit_version.md b/docs/subcommands/biscuit_version.md
@@ -7,12 +7,11 @@ permalink: /biscuit_version/
 
 # biscuit version
 ```bash
-BISCUIT Version: 1.4.0
+BISCUIT Version: 1.5.0
 
 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: 1.4.0
+Version: 1.5.0
 Contact: Jacob Morrison <[email protected]>
 
 Usage: biscuit <command> [options]