v0.16.0

Bismark

---

• File endings .fastq | .fq | .fastq.gz | .fq.gz are now removed from the output file (unless they were specified with --basename) in a bid to reduce the length of the already long file names.
• Enabled the new option --dovetail (which will be turned on by default for --pbat libraries) which will now allow dovetailing reads to be reported. For a more in-depth description see #14.
• Changed the behaviour of corner cases to where several non-directional alignments could have existed for the very same position but to different strands so that now the best alignment trumps the weaker one. As an example: If you relaxed the alignment criteria of a given alignment to allow ~60 mismatches for PE alignment we did find an alignment to the OT strand with a combined AS of -324, but there also was an alignment to the CTOB strand with and AS of 0 (perfect alignment). The CTOB now trumps the OT alignment, and the methylation information information is now reported for the bottom strand. Credits go to Sylvain Foret (ANU, Canberra) for bringing this to our attention!

New module: bismark2summary

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• bismark2summary accepts Bismark BAM files as input. It will then try to identify Bismark reports, and optionally deduplication reports or methylation extractor (splitting) reports automatically based the BAM file basename. It produces a tab delimited overview table (.txt) as well as a graphical HTML report.
  Examples can be found at http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_summary_report.html and http://www.bioinformatics.babraham.ac.uk/projects/bismark/bismark_summary_report.txt. Thanks to @ewels for help with the Java Script part!

New module: bam2nuc

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• The new Bismark module bam2nuc calculcates the average mono- and di-nucleotide coverage of libraries and compares this to the genomic average composition. bam2nuc can be called straight from within Bismark (option --nucleotide_coverage) or run stand-alone. bam2nuc creates a ...nucleotide_stats.txt file that is also automatically detected by bismark2report and incorporated into the HTML report.
  

bismark2_sitrep.tpl

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• Removed an extra function call in bismark_sitrep.tpl so that the M-bias 2 plot is drawn once the M-bias 1 plot has finished drawing (parallel processing could with certain browsers and data may have resulted in a white spaceholder only).

methylation extractor

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• Altering the file path handling of coverage2cytosine and bismark2bedGraph also required some changes in the methylation extractor.

bismark2bedGraph

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• Input file path handling has been completely reworked. The output file which can be specified as -o output.bedGraph now has to be a single file name and mustn't contain any path information. A particular output folder may be specified with -dir /any/path/.
• Addressing the file path handling issue also fixed a similar issue with the option --remove_spaces when -o had been specified.

coverage2cytosine

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• Changed zcat for gunzip -c when reading a gzipped coverage file. This should avoid some Mac platforms crashing because zcat invariably requires a file to end in the .Z (which it doesn't...)
• Changed the way in which the coverage input file is handed over from the methylation_extractor
  to coverage2cytosine (previously the path information might have been part of the file name, but
  instead it will now be only part of the -dir output_directory option.

v0.15.0

Bismark

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• Added option --se/--single_end <list>. This sets single-end mapping mode explicitly giving a
  list of file names as <list>. The filenames may be provided as a comma , or colon :-separated
  list.
• Added option --genome_folder <path/to/genome> as alternative to supplying the genome as the
  first argument.
• Added an option --rg_tag to print an @RG header line as well as and RG:Z: tag to each read.
  The ID and SAMPLE fields default to 'SAMPLE', but can be specified manually with --rg_id or
  --rg_sample.
• Added new option --ambig_bam for Bowtie2-mode only, which writes out a single alignment for
  sequences with multiple alignments to a special file ending in .ambiguous.bam. The alignments
  are in Bowtie2 format and do not any contain Bismark specific entries such as the methylation
  call etc. These ambiguous BAM files are intended to be used as coverage estimators for variant
  callers. Works for single-end and paired-end alignments in single or multi-core mode.
• Added the new options --cram and --cram_ref to Bismark for both paired- and single-end alignments
  in single or multi-core mode. This option requires Samtools version 1.2 or higher. A genome
  FastA reference may be supplied as a single file with the option --cram_ref; if this is not
  specified the file is derived from the reference FastA file(s) used for the Bismark run, and written
  to the file Bismark_genome_CRAM_reference.mfa into the output directory.

deduplicate_bismark

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• Added better handling of cases when the input file was empty (died for percentage calculation
  instead of calling it N/A)
• Added a note mentioning that Read1 and Read2 of paired-end files are expected to follow each
  other in two consecutive lines and possibly require name-sorting prior to deduplication. Also
  added a check that reads the first 100000 lines to see if the file appears to have been sorted
  and bail out if this is true.

methylation extractor

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• Added support for CRAM files (this option requires Samtools version 1.2 or higher)

bismark2bedGraph

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• Changed the way gzip compressed input files are handled when using the UNIX sort command (i.e. with
  --scaffolds/--gazillion or without --ample_memory

coverage2cytosine

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• Added option --gzip to compress output files. This currently only works for the default CpG_report
  and CX_report output files (and thus not with the option --gc or --split_files. The option --gzip
  is now also passed on from the bismark_methylation_extractor.
• Added a check to bail if no information was found in the coverage file, e.g. if a wrong file path for a .cov.gz file had been specified

bismark_genome_preparation

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• Added process handling to the child processes.

Bismark v0.14.5

20-08-2015: 0.14.5 released - minor fix

• deduplicate_bismark: Changed all instances of literal calls of samtools calls to $samtools_path