From 1e098a120f0ac57f8e6ab08db7fe35c13c0bd651 Mon Sep 17 00:00:00 2001 From: Owen Marshall Date: Thu, 7 Jan 2016 18:18:36 +0000 Subject: [PATCH] Updated changelog --- changelog | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/changelog b/changelog index d317631..7653a69 100644 --- a/changelog +++ b/changelog @@ -1,3 +1,26 @@ +[v1.4] +* New read-extension method: by default, reads are now only extended as far as the next GATC fragment. Use --extension_method=full to disable this feature and extend every read by the value of --len. +* Output format is now bedgraph by default. Use --output_format=gff to restore the previous default. Changing the default to bedgraph allows users to create TDF tracks directly within the graphical IGV tools, making it easier for end users. +* Minor code cleanups + +[v1.3] +* Major bugfix: reads from the minus strand were not being extended correctly during processing. The overall impact is minor (correlation between old and new read extension methods is >0.95) but this new method is technically more accurate. +* added --keep_sam (do not delete the temporary SAM file) option +* added --only_sam (do not generate BAM files) option (both options are intended for debug purposes only) + +[v1.2.7] +* New opition --no_file_filters to prevent any filename trimming/filtering (by default input filenames are trimmed to the first underscore) +* Small filename issue fixes + +[v1.2.6] +* Now uses File::Basename to handle filenames +* Fixed/cleaned up a number of rare problems with filename handling + +[v1.2.5] +* Added --dam and --out_name options. Use these to set the Dam-only control sample and/or a custom output name +* Added more sanity checks +* Minor bugfixes + [v1.2.4] * Added explicit checks for bowtie2 and samtools executables, and for bowtie2 output