- add: snp class, chromosme update
- mod: ld functionas are now in haplo_text
- upd: continued the process_file function translation
- marker_result_t has the pos in genome
- linkage_to_chromosome is now complete
- eliminated part of shared_options_t
- new params for haplodata
- renamed all functions in haplo_text to start with the name of the struct
- added t at the end of some structures
- check data params removed
- finished all methods
- moved some inlines from .c to .h in haplo_text
- began transition to marker_t without helper classes
- modified haplo_run to use the new structure
- fhandler became just a container w/o the function of file reading and processing
- transited from snp_t to marker_t
- ctor/dtor for marker_t
- mod some files to use the new vcf record
- modifying method to retrieve the alleles of a sample
- bug identified: instead of sample values, the reference and alternate were passed in different locations
- added method to set ref/alt
- modified the setting mechanism of samples in linkage_to_chr
- class chromosome to filter
- updating new structures
- new methods to get/set samples ref/alt
- replaced global.h with haplo.h
- fixed some compilation errors
- added support to determine the position of alleles for each SNP
- added support functions to get individuals
- changed the old method of getting values of alleles with the new one
- various modifications to include the bioformats library