exp007 - Influenza Data Processing

Age	Commit message (Collapse)	Author	Files	Lines
2010-01-25	Added the initialization of a sparse matrix to be used to track the	Don Pellegrino	6	-24/+127
	pairwise BLAST scores for all influenza sequences. Modified the Autoconf input so that libraries are automatically added to LIBS rather than manually in Makefile.am. Added the use of the PETSc API which is used for the sparse matrix implementation.
2010-01-24	Added library dependencies iherited from use of HDF5 on NCBI Cobalt including...	Don Pellegrino	2	-6/+8

2010-01-23	Added routines for loading BLAST scores.	Don Pellegrino	2	-0/+4

2010-01-19	Removed debugging flag. GNU Autotools is setting default debugging	Don Pellegrino	1	-1/+1
	(-g) and optimization flags (-O2) automatically. To override these exporting CFLAGS at ./configure time is necessary.
2010-01-18	Organzied the functions into assign, error, load and model subdirectories. C...	Don Pellegrino	22	-71/+181

2010-01-18	Implemented updator to calculate and assign protein type values to	Don Pellegrino	7	-96/+188
	records which do not have them. This is a re-entrant process that only updates missing records and skips quickly through existing records. In addition premature termination loses at most 999 records of work since every thousand records are written back to the file and flushed to disk. Still to do is to write and flush the last set of records in the final bin under 1000. Also refactored the sequence_data structure so that it can be shared between HDF5 reading and writing operations.
2010-01-18	Moved updating the HDF5 file to a separate driver.	Don Pellegrino	3	-8/+43

2010-01-17	Added error checking routines. Added implementation of	Don Pellegrino	12	-13/+211
	assign_protein_type tested against a single hard-coded sequence input. The next step is to iterate over all records in the HDF5 collection that don't have a type assigned and to assign a type value.
2010-01-16	Added the assign_protein_type function declaration without implementation.	Don Pellegrino	1	-0/+2

2010-01-16	Added function declaration for load_influenza_faa.	Don Pellegrino	4	-3/+31

2010-01-15	Code compiles and creates an HDF5 file containing a table with one	Don Pellegrino	5	-0/+208
	record of influenza_aa.dat populated.