Allow minirmd to run on .fasta files #2
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Patches a segfault that occurs when sequences are longer than the first sequence in a file. Minimal performance hit to check all string lengths. Elapsed time for max_strlen: 0.331280s This was to find the longest sequence for 13,835,165 sequences
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Part of a series of commits which will patch minirmd to properly function on input with unequal sequence lengths. With the above patch it is functional, but will miss a small amount of duplicates. No improper culls were observed. |
optional -l arg allows the user to specify where they would like the duplicates removed to go. Additionally, if the input/output is a fasta file sequence headers now start with a >. If the input/output is a fastq file sequence headers still begin with a @
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Duplicates removed are clustered by the parent sequence and header. Parent sequence headers end with a . for easy identification. Subsequent headers and sequences are duplicates of said parent and header pair. This remains true until the next header ending with a . is found. |
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Patches a segfault that occurs when sequences are longer than the first sequence in a file. This allows minirmd to run on .fasta files.
Minimal performance hit to check all string lengths.
Elapsed time for max_strlen: 0.331280s
This is the time it took to find the longest sequence for 13,835,165 sequences in a fasta file.