Merge branch 'master' into Haploflow-test1

cfe-lab · Sep 25, 2023 · d0407a8 · d0407a8
2 parents 5ecb109 + 3f791c5
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diff --git 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
@@ -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'}