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# SamSifter Help

## Manual

- SamSifter Manual
  - Detailed Installation Instructions
    - Installing `Python3` and `PyQt4`
      - Debian 8 (jessie) and newer or Ubuntu 14.04 and newer
      - Older Debian or Ubuntu systems
      - Mac OS X using Homebrew
      - Windows (32 bit)
    - Installing SamSifter
    - Uninstalling SamSifter
  - Creating and Editing Workflows
    - Selecting an Input File
    - Adding and Removing a Tool or Filter
    - Rearranging Tools and Filters
    - Displaying and Editing Filter Settings
    - Selecting an Output File
      - Optional: Creating an RMA file for MEGAN
  - Executing Workflows
    - Running a Workflow
    - Log Messages
    - Stopping a Workflow
  - Loading and Saving Workflows
  - Export to Bash scripts
  - Manuals for Filters and Tools
    - Common Options
    - Count reads per taxon
    - Filter reads by conservation
    - Filter reads by list of QNAMES
    - Filter references by evenness of coverage
      - What is the Gini coefficient?
      - Experimental options
    - Filter references by % identity
    - Filter references by list of accessions
    - Filter references by PMD score
    - Filter taxa by list of taxon IDs
    - Filter taxa by PMD score
    - [GNU gzip] Compress file
    - [GNU gzip] Decompress file
    - [PMDtools] Calculate PMDS
    - [PMDtools] Filter reads by % identity
    - [PMDtools] Filter reads by PMDS
    - [SAMtools] Convert BAM to SAM
    - [SAMtools] Convert SAM to BAM
    - [SAMtools] Remove duplicates
    - [SAMtools] Sort by coordinates
    - [SAMtools] Sort by query names
    - [BetterRMDup] Remove duplicates
  - Statistical Summaries
    - Compiling Results Per Analysed File
    - Comparison of Multiple Files
    - Enriching Summaries with External Databases

## Frequently Asked Questions

None so far...

## Known Bugs

Please report new bugs to samsifter@biohazardous.de.

### Bugs in SamSifter

- The filter direction parameter of some filters, especially the ‘Filter taxa by list’ filter, should be moved from the optional to the required tab to avoid confusion, eg. when running the human pathogen screening workflow.
- Exported bash scripts will attempt to execute SAM2RMA even if this option was disabled in the GUI. In combination with the ‘Stop on error’ option the script will fail silently on systems without SAM2RMA in their `$PATH` because of the `which sam2rma` in the bash script’s first lines. Workaround: comment out the optional SAM2RMA commands or install MEGAN incl. SAM2RMA.

### Bugs in Tools used by SamSifter

- BetterRMDup fails when processing MALT’ed files. This is actually a bug of the SAM parsing library used in BetterRMDup that does not handle the custom MALT `@mm` record properly. The bug has been reported and will be fixed in a future version.
- SAMtools `view` reports a possibly truncated file and complains about a missing EOF marker. This is likely a bug in either MALT and/or SAMtools `view` which can be safely ignored. See http://sourceforge.net/p/samtools/mailman/samtools-help/thread/4EC52844.3090808@broadinstitute.org/ for details. It is caused by a missing compression flag when processing uncompressed files.
- SAMtools `view` complains about inconsistency of the sequence length when compared to the CIGAR string. This is a bug in MALT 0.0.12 that has been reported. Please re-MALT your files with a newer version or remove the affected reads manually.

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