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Seqal Counters

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Seqal Properties

Seqal has a number of properties that configure its operation. You may need to change some of the default values to make Seqal work for you the way you want. These settings can be set on the command line with the -D option (see Program Usage for details) or they can be set in a Seal configuration file (see Seal Config File).


Config File Section Title: Seqal

Logging level. This value is used to configure the logging module used by Seqal. Its value must be one of: CRITICAL, ERROR, WARNING, INFO, DEBUG. Default value: ‘INFO’.
If the inferred insert size is greater than this value, Smith-Waterman alignment for unmapped reads will be skipped. Default value: 1000.
The number of sequences to be processed at a time by alignment functions. The batch size influences the insert size statistics (bigger should give more accurate estimates). However, increasing the batch size increases memory usage, and increasing it too much will result in Hadoop task timeouts. Default value: 10000.
Specifies base quality score encoding. Supported values are ‘fastq-sanger’ for base qualities encoded in Sanger Phred+33 format (ASCII range 33-126) and ‘fastq-illumina’ base qualities encoded in Illumina Phred+64 format (ASCII range 64-126). Default value: ‘fastq-illumina’.
Minimum mapping quality (mapq) score. Mappings with mapq below this threshold will be discarded. Default value: 0.
Discard unmapped reads. Default value: false.
Discard duplicate reads. If true, Seqal will only keep the duplicate read or read pair with the best average base quality. If false, the duplicates will be marked by setting the duplicate bit (0x0400) in the SAM flag. Default value: false.
Number of threads to use when finding the SA coordinates of the input reads. We recommend this value be left at 1. To take advantage of multi-core machines configure appropriately the number of Hadoop map tasks per node. Default value: 1.
q-value for read trimming. This is equivalent to the -q BWA option. You can also specify the value of this property with the --trimq command line option.

Deprecated Properties

All the properties defined in the first versions of Seqal have been renamed, from bl.seqal.* to seal.seqal.*. The old property names have been deprecated, but for the time being will be accepted with a warning. Future versions of Seal will ignored them altogether, so you are urged to update your scripts or configuration files. The table below presents the complete list of deprecated Seqal properties.

The following properties, recognized in previous versions of Seal, have been deprecated and replaced. They are still functional for the moment, but will be completely removed in future versions so you are urged to update your configurations and scripts.

Deprecated property Replacement
bl.seqal.log.level seal.seqal.log.level
bl.seqal.alignment.max.isize seal.seqal.alignment.max.isize
bl.seqal.pairing.batch.size seal.seqal.pairing.batch.size
bl.seqal.fastq-subformat seal.seqal.fastq-subformat
bl.seqal.min_hit_quality seal.seqal.min_hit_quality
bl.seqal.remove_unmapped seal.seqal.remove_unmapped
bl.seqal.discard_duplicates seal.seqal.discard_duplicates
bl.seqal.nthreads seal.seqal.nthreads
bl.seqal.trim.qual seal.seqal.trim.qual
bl.seqal.log.level seal.seqal.log.level
bl.seqal.discard_duplicates seal.seqal.discard_duplicates