Package: wnpp Severity: wishlist Owner: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org>
* Package name : dazzdb Version : 1.0 Upstream Author : Eugene W. Myers, Jr. <gene.my...@gmail.com> * URL : https://github.com/thegenemyers/DAZZ_DB * License : BSD Programming Lang: C Description : database library for the dazzler assembler To facilitate the multiple phases of the dazzler assembler, all the read data are organized into what is effectively a "database" of the reads and their meta-information. The design goals for this database are as follows: (1) The database stores the source Pacbio read information in such a way that it can recreate the original input data, thus permitting a user to remove the (effectively redundant) source files. This avoids duplicating the same data, once in the source file and once in the database. (2) The database can be built up incrementally, that is new sequence data can be added to the database over time. (3) The database flexibly allows one to store any meta-data desired for reads. This is accomplished with the concept of *tracks* that implementors can add as they need them. (4) The data is held in a compressed form equivalent to the .dexta and .dexqv files of the data extraction module. Both the .fasta and .quiva information for each read is held in the database and can be recreated from it. The .quiva information can be added separately and later on if desired. (5) To facilitate job parallel, cluster operation of the phases of dazzler, the data base has a concept of a *current partitioning* in which all the reads that are over a given length and optionally unique to a well, are divided up into *blocks* containing roughly a given number of bases, except possibly the last block which may have a short count. Often programs con be run on blocks or pairs of blocks and each such job is reasonably well balanced as the blocks are all the same size. One must be careful about changing the partition during an assembly as doing so can void the structural validity of any interim block-based results.
