Pear library license

It also captures the log output and reformats the output to a tab-delimited format both logs are captured. Added --version options Fixed minor error when loading bzip files Lowered autotools version. An updated version of PEAR is released. Added zlib support Renamed options from --left-fastq and --right-fastq to --forward-fastq and --reverse-fastq, respectively. Added --nbase option that places an N as the result of merging when the base-pair to be merged consists of two different, non-degenerate bases Updated man-pages with the new options.

Replaced assertion when the paired-end read has no overlap but still passes the statistical test. Added checks whether output files are writable Fixed condition to allow 1 base long reads. Capped the quality scores of the overlapping region Minor bug fixes.

This package reimplements some of the code that is being provided on pear. Unfortunately none of these provide anything near a decent and usable developer API. One could hope for the newer Pyrus code to resolve some of the deeper structural problems the PEAR code has.

The currently available code as of does not look like a major improvement though. But the amount of hacks and workarounds required to sustain that basis was too much for a long term solution.

Skip to content. Star 0. A library for handling a subset of the PEAR formats and specifications www. The optional arguments affect the process of assemblying. PEAR outputs four files.

A file containing the assembled reads with a assembled. If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Valid options are: 0. Setting 1.

Specify the minimum overlap size. The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. Specify the maximum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long.

Specify the minimum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. Specify the minimum length of reads after trimming the low quality part see option -q. Specify the quality score threshold for trimming the low quality part of a read. If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. Specify the maximal proportion of uncalled bases in a read.

Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases.