From a4420a8c4762c6a7a85984f38bf396acb0987b9b Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Tue, 12 Sep 2023 11:12:59 -0700 Subject: [PATCH 1/3] add HIV-AD option to utils/primer_locations script --- micall/utils/primer_locations.py | 1 + 1 file changed, 1 insertion(+) 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'} From f06d1c9ac85f75c76c4d1b3c694a048c4a705495 Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Tue, 12 Sep 2023 12:51:17 -0700 Subject: [PATCH 2/3] docs: describe genome.pos field of nuc.csv output --- docs/steps.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/steps.md b/docs/steps.md index 04aeb9651..f33115d8b 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, relative + to the beginning of the entire reference sequence. Unlike + refseq.nuc.pos, this is not is 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 From cf6761507c2ed155249d75c29c06375ea6f1effc Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Tue, 12 Sep 2023 13:04:16 -0700 Subject: [PATCH 3/3] docs: fix typo in steps.md --- docs/steps.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/steps.md b/docs/steps.md index f33115d8b..57d0695c9 100644 --- a/docs/steps.md +++ b/docs/steps.md @@ -322,9 +322,9 @@ 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, relative - to the beginning of the entire reference sequence. Unlike - refseq.nuc.pos, this is not is specific to a single gene or + * 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