elPrep Binaries

elPrep binaries compiled with Go.1.12.2.

Added graph algorithm for optical duplicate marking.
Added additional histogram metrics in duplicate marking metrics.

elPrep Binaries

elPrep binaries compiled with Go.1.11.5.

Bug fix:

There was an issue when the --replace-reference-sequences option was used with the elprep sfm command, which under certain circumstances may have resulted in improperly sorted results. This has been fixed in elprep version 4.1.1. Thanks a lot to Geert Vandeweyer for reporting this issue.

Additional fixes:
- The --replace-reference-sequences option incorrectly removed unmapped reads. This has been fixed in version 4.1.1 and does not happen anymore.
- The --contig-group-size option has been deprecated for the elprep merge command. The elprep sfm and elprep split command still support it. The elprep split command now works correctly without knowing the --contig-group-size that was passed to the corresponding elprep split command.
- The BGZFWriter panicked when a Write happens after a Close because of sending data to a closed Go channel. This has been changed into a proper error return value.

elPrep Binaries

elPrep binaries compiled with Go.1.11.4

Turned pixel distance for optical duplicate marking into a parameter.

elPrep Binaries

elPrep binaries compiled with Go.1.11.1

Fixed a bug in the fasta parser.

If you see an error message that says "panic: runtime error: slice bounds out of range" that refers to a location in github.com/exascience/elprep/v4/fasta.OpenElfasta, then please recreate the corresponding .elfasta file with the fasta-to-elfasta command to fix this error.

Various minor fixes.

elPrep Binaries

elPrep binaries compiled with Go.1.11.1

elPrep 4.0.0 release.

• added base quality score recalibration (BQSR)
• added optical duplicate marking
• added metrics (MultiQC compatible)
• support for SAM File Format version 1.6
• support for FASTA and VCF files
• support for BAM/BGZF files
• support for elPrep-specific elsites and elfasta formats
• split/filter/merge (sfm) mode now implemented in Go instead of Python
• added --log-path option to all tools
• various API and performance improvements
• changed license to the GNU Affero General Public License version 3 as published by the Free Software Foundation, with Additional Terms
• updated demos

elPrep Binaries

elPrep binaries compiled with Go1.10.3

Added new filter:
--filter-mapping-quality mapping-quality for filtering out reads based on mapping quality.

elPrep should now be able to handle long reads.

Various bug fixes/improvements:

• fixed bugs for handling .cram files
• improved error handling
• various code clean ups

Many thanks to Leonor Palmeira, Matthias De Smet, and Koen Herten for bug reports/suggestions.

elPrep Binaries

elPrep binaries compiled with Go 1.9.2.

Added 3 new filters:
--filter-non-overlapping-reads bed-file: Removes all reads of which the positions do not overlap with any region specified in a given .bed file.
--remove-optional-fields [all | list]: Removes from reads either all optional fields or all optional fields specified in a given list.
--keep-optional-fields [none | list]: Removes from reads either all optional fields or all optional fields except those specified in a given list.

Added .bed file parsing and representation.

Fixed minor bug with PG header lines.

Many thanks to Leonor Palmeira for testing.

elPrep Binaries

elPrep binaries compiled with Go 1.9.1.

The split/merge tools can now handle single-end data. For this, the elprep split and merge commands have been extended with the --single-end option. Similarly, the split/filter/merge scripts have been changed to allow the use of the --single-end option.

Many thanks to Geert Vandeweyer for bug reports.

elPrep Binaries

elPrep binaries compiled with Go 1.9.1.

--mark-duplicates now compares reads using the library id instead of just the read group id, matching the behaviour of picard-2.13.2

The spliter/filter/merge scripts have been changed:

• to be able to handle a directory as input
• added a --intermediate-files-output-prefix option to specify the name of the intermediate output files generated by the elprep split call
• to have the default file type of the intermediate output files be derived from the file type of the input (sam/bam/cram)

Optimisation for reducing the memory footprint (where possible).

Many thanks to Geert Vandeweyer for bug reports.

elPrep Binaries

elPrep binaries compiled with Go 1.9.

Added two new filters:
--filter-non-exact-mapping-reads
--filter-non-exact-mapping-reads-strict
for removing all reads where the mapping is not an exact match with the reference, based on the cigar string or optional tags, see documentation.

Fixed minor bug:
-mark-duplicates filter no longer requires adding read groups to execute

Added API documentation in the source code.

Many thanks to Leonor Palmeira for bug reports.