PALEOMIX v1.3.8

Fixed

• Added 'genotyping' alias to match phylo pipeline documentation (issue #48).
• Fixed options for BWA aln being applied to samse and sampe (issue #49).

PALEOMIX v1.3.7

Added

• Added example to BAM pipeline YAML template, showing how to increase the maximum
  allowed Phred score for AdapterRemoval. This is needed due to the value being
  capped at 41 by default, lower than the maximum observed in some modern data.

Fixed

• Fixed regression in config file parsing, that would cause failure if no value
  was specified for an option.
• Fixed error message not being printed correctly when attempting to use Phred+64
  data with BWA mem/bwasw.
• Fixed regressions that prevented the use of "regions of interest" in the BAM
  pipeline.
• Fixed failure when using --list-output-files and auxilary files were missing
  or dependecies were unmet. Output files are now printed.

PALEOMIX v1.3.6

Added

• Added explicit support for the AdapterRemoval --trim5p and --trim3p options,
  which may take one or two values (as a list).

Changed

• User options for AdapterRemoval are no longer restricted by a whitelist.

PALEOMIX v1.3.5

Added

• Added command-line option to reduce/turn off validation with picard ValidateSamFile.

PALEOMIX v1.3.4

Added

• Added support for the --collapse-conservatively AdapterRemoval option.

Changed

• Avoid creating log files on invalid commandline arguments.
• The directory for the log-file is created automatically if it does not exist.
• No longer prints stack-trace if the user terminates a pipeline wiht Ctrl + C.
• Log-level command-line options are now case insensitive.
• The default number of threads used by AdapterRemova, Bowtie2, and BWA are now scaled
  based on the available number of cores instead of defaulting to 1 thread.
• Less exhaustive validation of .bai index files using picard ValidateSamFile. The
  overhead of validating these files was excessive in light of the small benefit.

Fixed

• Fixed regression causing certain option to not be applied when mapping with BWA.
• Fixed --log-level not having an effect.
• Fixed possible infinite recursion when using lazily created log-files.
• Fixed BAM pipeline failing if mapDamage feature was not explicitly set.
• Fixed default values of 0 or 1 not being listed in commnad-line help text.

PALEOMIX v1.3.3

Fixed

• Fixed regression in BAM pipeline summary node, causing failing if there were zero
  hits or reads.
• Fixed BAM validation always being run in big-genome mode, resulting in some checks
  being disabled despite being applicable.

PALEOMIX v1.3.2

Minor bug-fix release.

Added

• Added -v and --version to all command-line tools.
• Added the default values (if any) to the help-strings of all command-line options.

Changed

• Decoupled --log-level from command-line logging. Changed default log-level to
  ERROR and made it apply to automatically generated log files as well.

Fixed

• Fixed the pipeline failing on jre_options (now jre-option) in config files.
• Fixed the pipeline failing on empty options in config files from PALEOMIX v1.2.x.
• Fixed Bowtie2 using command-line options from the BWA makefile section
• Fixed conda installation instructions and environment file for PALEOMIX 1.3.x.

PALEOMIX v1.3.1

Minor bug-fix release.

Fixed

• Updated shebangs to 'python3'. Patch courtesy of Andreas Tille.
• Added minimal support for previously removed command-line options, to prevent the
  pipelines from failing when used with old configuration files.

PALEOMIX v1.3.0

PALEOMIX v1.3.0 is a major maintenance release, with the goal of porting PALEOMIX to
Python 3 and to prepare for further work to update and expand the pipeline. A number of
deprecated tools and options have been removed, as has support for very old versions of
tools used by the pipelines.

Existing makefiles are compatible with PALEOMIX 1.3.0 with a few notable exceptions:

• BAM pipeline support for the GATK Indel Realigner has been removed, and the options
  'RealignedBAM' and 'RawBam' no longer have any effect. These are now simply ignored
  and a "raw" BAM is always produced. The Indel Realigner tool was removed from GATK
  as of GATK4 (released 2018) and continued support is not deemed worthwhile due to the
  minor benefit from running the Indel Realigner.
• BAM pipeline support for generating PCR duplicate histogram files for use with PreSeq
  has been removed. The option is simply ignored.
• BAM pipeline support for AdapterRemoval options --pcr1 and --pcr2 has been removed,
  as these options are long deprecated and will be removed from AdapterRemoval. Use the
  --adapter1 and --adapter2 options as described in the BAM pipeline documentation.
• Phylo pipeline options for BCFTools must be be updated to replace the option invoking
  the consensus caller ("-g") with "-c", or with "-m" for the multiallelic caller.
• The Phylo pipeline genotyping methods 'Random Sampling' and 'Reference Sequence' are
  no longer supported.

Please open an issue if features or options import to your work have been removed.

Added

• The BAM and Phylo pipelines print warnings when deprecated/removed options are used
• A log-file is automatically created if errors are encountered during run-time.

Changed

• Converted project from Python 2.7 to Python 3.5+.
• Removed internal copy of pyyaml and added dependency on ruamel.yaml.
• Command-line output was changed to a simpler, log-log output using coloredlogs.
• Bumped minimum version requirements for most tools used by the pipelines; minimum
  versions were largely informed by availability in Debian stretch.
• Changed naming of BAM index files created by the BAM pipeline from 'filename.bai' to
  'filename.bam.bai' in order to match the behavior of standard tools (e.g. samtools).
• The filenames of input FASTQ files are now used in the intermediate file-structure,
  with the goal of making the pipeline more robust to changes in input files.
• The pipeline no longer fails if a command generates more files than expected,
  instead this merely triggers a warning.
• Moved PCR duplicate filtering and rescaling to 'Features' in BAM pipeline makefiles.

Fixed

• Fixed spurious warnings from pysam (htslib) when opening BAMs without index files.

Removed

• Removed limited support for 32 bit systems
• Removed the 'cat' command.
• Removed the 'duphist' command and the corresponding BAM pipeline feature.
• Removed the 'ena' command.
• Removed the 'sample_pileup' command.
• Removed the 'retable' command. A more performant standalone version can be found at
  https://github.com/MikkelSchubert/retable
• Removed the bam_pipeline 'remap' command.
• Removed entry-points other than the 'paleomix' command; that is to say the stand-
  alone 'bam_pipeline', 'phylo_pipeline', etc. commands.
• Removed data for the original publication of PALEOMIX. The instructions in that
  publication are outdated and cannot be carried out for current versions of PALEOMIX.
• Removed support for configuration files with per-host sections. Files are now
  assumed to contain only one set of command-line options.
• Removed --to-dot option for pipelines.
• Removed keyboard shortcuts for modifying pipeline behavior during runtime.
• Removed undocumented options from Zonkey.
• Removed undocumented codeml support from the Phylo pipeline.
• Removed 'Random Sampling' and 'Reference Sequence' genotyping methods.
• Removed makefile metadata (filename, hash, mtime) from BAM pipeline summary reports.
• Removed support for compressing intermediate FASTQ files using bzip2. Reads are now
  always compressed using gzip.
• Removed ability to merge FASTQ files with the the SplitLanesByFilenames option.
  Files are now always split, meaning that individual FASTQ files or pairs are mapped.
• Removed support for indel realignment using GATK due to its removal from GATK.
• Removed creation of FASTA sequence dictionaries as they were only needed by GATK.
• Removed support for labels for BAM pipeline prefixes.

PALEOMIX v1.2.14

Changed

• Improved handling of K-groups in zonkey database files
• Change BAM pipeline version requirement for GATK to < v4.0, as the
  the Indel Realigner has been removed in GATK v4.0

Fixed

• Fixed version detection of GATK for v4.0 (issue #23)