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Update Version 1.0.0

mstatspop now accept tfasta file in version 2 compressed with htslib (bgzip) and indexed format (.tbi).

Implementation

mstatspop now uses htslib to read and write Files,the input tfasta file/weight files is compressed (bgzip) and indexed. The tfasta index file is created with htslib tabix format.

TFasta file format

The tfasta file format has the following format:

##fileformat=TFAv2.0
# command1 
# command2
#NAMES: >chr1_a >chr1_b .....
#CHR	POSITION	GENOTYPES
chr10	31338	GGGGNNGGGGGGGGGGGGGGGGGGGGGGGGGGNNGGGGGGGG
chr10	31339	GGGGNNGGGGGGGGGGGGGGGGGGGGGGGGGGNNGGGGGGGG
chr10	31340	AAAANNAAAAAAAAAAAAAAAAAAAAAAAAAANNAAAAAAAA
chr10	31341	TTTTNNTTTTTTTTTTTTTTTTTTTTTTTTTTNNTTTTTTTT
chr10	31342	AAAANNAAAAAAAAAAAAAAAAAAAAAAAAAANNAAAAAAAA
chr10	31343	CCCCNNCCCCCCCCCCCCCCCCCCCCCCCCCCNNCCCCCCCC
chr10	31344	TTTTNNTTTTTTTTTTTTTTTTTTTTTTTTTTNNTTTTTTTT
chr10	31345	GGGGNNGGGGGGGGGGGGGGGGGGGGGGGGGGNNGGGGGGGG

Header section:

  • ##fileformat=TFAv2.0 : The version of the tfasta file format.
  • #command1: The command used to generate the tfasta file.
  • #command2: other command used to generate the tfasta file.
  • #NAMES : The names of the sequences in the tfasta file. The names are separated by a space and start with the ">" character.

Data section is a tab-separated file with the following columns:

  • CHR: Chromosome name
  • POSITION: Position in the chromosome
  • GENOTYPES: Genotypes in the position. The genotypes are represented by the IUPAC nucleotide code. Missing data is represented by N.

Weight file format

The weight file format aslo follow the same fomat with extra columns