i would like to extract the name of chromosome and the relative bases, for all the fasta file(22 chromosomes).
for example
"chr1
AACTTAGCCC......
chr2
CCAAAATCGG......
.... "
but i need the code, because then i' ve to working with the information to compare with a bam file.
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TwoFaces •
I just compiled and ran the code without problems on a FASTA file with the suffix .fa. I don't think the suffix is the issue. Are you sure you have a valid FASTA file?
Yes, i use the standard human hg19.fasta, plus i've got the .fasta.fai, but i don't know how to use it.
FASTQ format is NOT the same as FASTA format
If I remember correctly, that library is supposed to work with either type.
I initially thought that too, but the web page states that kseq.h parses "both FASTA and FASTQ format, and even a mixture of FASTA and FASTQ records in one file."
then that code doesn't work with a .FASTA file...
Yes it does, as I stated in my first comment.
So, i ran it with "nameofprogram file.fasta" and returns "return value -1".
the problem is that when i insert the fasta, fp = NULL ( fp = gzopen(argv[1], "r"); ), and in zlib.h says that "gzopen returns NULL if the file could not be opened or if there was insufficient memory to allocate the (de)compression state"