This release significantly updates the user interface, focusing on making option names more consistent and logical. Additionally some new functionality has been added, and a few bugs fixed.
The tables below give an overview of old and new option names for those options that have changed, divided into the 7 argument groups used when printing the command line help.
Overview of changes in user-interface
Input/Output
| Old Option | New Option | Comments |
| :------------- | :---------------- | :-------- |
| seqconverter [...] SEQFILE | -i SEQFILE | Input file was originally positional argument, but is now specified with -i |
| -I FORMAT | --informat FORMAT | Default is to autodetect, so can often be omitted |
| -O FORMAT | --outformat FORMAT | Default output format is fasta, so can be omitted in that case<br>Removed nexusgap as possible output format - rarely used,<br> and will create new options for gapencoding instead |
Selecting subset of sequences
| Old Option | New Option | Comments |
| :------------- | :---------------- | :-------- |
| --subsample N | --sampleseq N | |
| --select "REGEXP" | --keepreg "REGEXP" | |
| --discard "REGEXP" | --remreg "REGEXP" | |
| --subset NAMEFILE | --keepname NAMEFILE | |
| --remseqs NAMEFILE | --remname NAMEFILE | |
| --filterpos<br> VARIANT[,VARIANT,...] | --keepvar VARIANT [...] | |
| --filterdupseq | --remdupseq | In v3.0.0: no longer prints names of removed sequences on stderr <tr></tr> |
| --filterdupname | --remdupname | |
Selecting subset of positions in sequences
| Old Option | New Option | Comments |
| :------------- | :---------------- | :-------- |
| | --samplecols N | New in 3.0.0: Randomly select N columns from alignment |
| --subseq START.STOP | --keepcols INDEX_OR_RANGE [...] | Example: --keepcols 10 15 22-40 57 |
| --remcols INDEX-LIST | --remcols INDEX_OR_RANGE [...] | Example: --remcols 10 15 22-40 57 |
| --remgapcols<br> --remallgapcols<br> --remfracgapcols FRAC | --remgapcols [FRAC] | Covers all variants. <br>If FRAC not given: remove column if any gaps. <br>If FRAC given: remove column if >= FRAC fraction gaps |
| --remambigcols | --remambigcols [FRAC] | Now works like the new --remgapcols [FRAC] command.<br> If FRAC not given: remove column if any ambiguity symbols. <br>If FRAC given: remove column if >= FRAC fraction <br>ambiguity symbols |
| --remendgapcols FRAC | --remendgapcols [FRAC] | Now works the same way as two options above |
| --remhmminsertcols | | Remove option which is rarely used.<br>User can directly use sequencelib if function needed. |
Renaming sequences
| Old Option name | New Option Name | Comments |
| :-------------: | :----------------: | :-------- |
| --renamenumber | --renamenum | |
| --appendnumber | | Removed rarely used option |
| --renameregexp "REGEXP" | --renamereg <br>"OLD_REGEX" "NEW_STRING" | Shortened name.<br>In new version user can provide replacement string (old version always deleted regex) |
| --regdupfix | | Removed: now fails with error message indicating duplicate created |
| --savenames FILE | --saverename NAMEFILE | |
| --restorenames FILE | --renamefile NAMEFILE | |
Combining multiple sequence files
| Old Option name | New Option Name | Comments |
| :-------------: | :----------------: | :-------- |
| --overlap<br>--minoverlap N | --overlap [MIN] | Optional value MIN can now be given directly to --overlap |
| --mbpartblock | --mb | |
DNA manipulations
| Old Option name | New Option Name | Comments |
| :-------------: | :----------------: | :-------- |
| --translate | --translate<br> READING_FRAME | User can now specify in which reading frame to perform translation |
Summaries
| Old Option name | New Option Name | Comments |
| :-------------: | :----------------: | :-------- |
| --seqcom | --comseq | |
Bug fixes
- Fixed bug where automatic fileformat detection did not work when input was on stdin
- Fixed bug where --overlap did not work
- Fixed bug where --paste did not work