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ogotoh / spaln

Genome mapping and spliced alignment of cDNA or amino acid sequences
GNU General Public License v2.0
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sortgrcd is only reporting one alignment #18

Open jwasmuth opened 5 years ago

jwasmuth commented 5 years ago

Hi, I am using sortgrcd v2.1. I am finding potentially strange behaviour when I output in any of the newly supported formats (-O 3, 6, 7, 8). If more than one target sequence hits a particular region of the genome, I receive only one alignment. I'm not sure how the alignment is selected from the other overlapping alignments - it is not the highest scoring. When I use other output formats, e.g. -O 0 or 5, I get all the alignments. This is the behaviour I would prefer from -O3 and others. Perhaps include an option in sortgrcd to keep the best scoring if alignments overlap? Thanks James

ogotoh commented 5 years ago

Please use -E2 option. This information has been added in the help message of sortgrcd.