diff --git a/docs/steps.md b/docs/steps.md index 04aeb9651..57d0695c9 100644 --- a/docs/steps.md +++ b/docs/steps.md @@ -322,6 +322,10 @@ Individual files are described after the list of steps. contig that the reads were mapped to * refseq.nuc.pos - the 1-based index of the base in the coordinate reference for a single gene region on non-coding region, named in the region column + * genome.pos - the absolute 1-based index of a nucleotide (in other words, + relative to the beginning of the entire reference sequence). This is the same + as refseq.nuc.pos, but not specific to a single gene or + non-coding region. * A,C,G,T - counts for the nucleotides at this position * N - count of reads with Phred quality score below the cutoff * del - count of reads with a deletion at this position diff --git a/micall/utils/primer_locations.py b/micall/utils/primer_locations.py index ab03c285e..b497258c4 100644 --- a/micall/utils/primer_locations.py +++ b/micall/utils/primer_locations.py @@ -8,6 +8,7 @@ from micall.utils.alignment_wrapper import align_nucs PRIMER_SETS = {'HIVB': 'HIV1-B-FR-K03455-seed', + 'HIV-AD': 'HIV1-B-FR-K03455-seed', 'HIVGHA': 'HIV1-B-FR-K03455-seed'}