diff --git a/docs/releases.md b/docs/releases.md index b576fd6..5a1a6c5 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 1.4.0** + - **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 index 32ea0d1..c3002a9 100644 --- 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 index fc1b3c0..f9cda86 100644 --- 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 index 53630fb..c3ed442 100644 --- 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 index 749a49a..c32cf6b 100644 --- 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 index 94c6063..47319e7 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: 1.4.0 +Version: 1.5.0 Contact: Jacob Morrison Usage: biscuit [options]