| Class | Description |
|---|---|
| ColumnsToBinaryFullGenomeTablePlugin |
This plugin is copied from the ColumnsToBinarySNPOnlyTablePlugin (which was copied Kelly's ColumnsToBinaryPlugin, which re-worked various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGEnomeDB of the Rare Alleles monetdb instance. THe difference between this plugin and the ColumnsToBinarySNPOnlyTablePlugin is the latter creates entries only for identified hmp321 SNPs This method (ColumnsToBinaryFullGenomePlugin) creates entries for all positions listed in in the reference genome. To be consistent with the existing columns in monetdb maize tables, the reference file must be a link to a copy of the Zea_mays.AGPv3.20.dna.genome.fa file stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files. This plugin may also be used to create binaries for the maizeChrom10DB. In this case, we still use the full reference genome, but only chrom 10 is processed. The inputFile paramaeter shoudl be just 1 file containing chromosome 10 data.
|
| ColumnsToBinarySNPOnlyTablePlugin |
This plugin is copied from Kelly's ColumnsToBinaryPlugin (which was re-worked from various lynn methods) to create binary files for loading into the hmp321_snp table in the maizeFullGenomeDB of the Rare ALleles monetdb instance. THe difference between this plugin and the ColumnsToBinaryFullGenomeTablePlugin is the latter creates entries for all positions listed in the reference genome. This method only creates entries positions identified as SNPs from hmp321. To be consistent with the existing columns in monetdb, the reference directory must be a link to a directory that contains copies of the SNPPos_chromX.txt files stored on andersonii in Research/Zea/Genotypes/Annotations/monetDB/refGenomeFiles. The "inputFile" parameter can be either a single file containing data for all chromosomes or a directory of files split by chromosome. If all chroms are in a single file, that file must be sorted by chromosome and position, and must contain a header line that contains the columns "chr" and "pos" along with user specified data columns. If the "inputFile" parameter is a directory, the only *.txt files it holds must be files intended for this processing. These files must be split by chromosome and must be named such that they will sort lexicographically in chromosome order. For example: files named chr01.txt, chr02.txt ... chr09.txt, chr10.txt will sort from 1-10. But files named chr1.txt, chr2,txt ... chr9.txt, chr10.txt will not. In the latter case, chr10.txt will be processed before the other files.
|
| ColumnsToBinaryUtils |
This class contains utility functions to aid in creating monetdb binaries
|
| LittleEndianDataOutputStream |
Monetdb used LittleEndian format while java writes to BigEndian This class writes the binary files to accepted monetdb format.
|