From 69e36299168d739dded1c5549f662793af10da83 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Wed, 22 May 2024 12:58:33 -0700 Subject: [PATCH] Mention in man page that CIGAR strings in SA tags are approximate (#1213) * Mention approx CIGAR strings in man page #724 * Fix FAQ typo --- FAQ.md | 2 +- minimap2.1 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/FAQ.md b/FAQ.md index 94a1bbce..d2ce9da3 100644 --- a/FAQ.md +++ b/FAQ.md @@ -2,7 +2,7 @@ Without `-a`, `-c` or `--cs`, minimap2 only finds *approximate* mapping locations without detailed base alignment. In particular, the start and end -positions of the alignment are impricise. With one of those options, minimap2 +positions of the alignment are imprecise. With one of those options, minimap2 will perform base alignment, which is generally more accurate but is much slower. diff --git a/minimap2.1 b/minimap2.1 index 9e15ccdd..f8abbc7a 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -742,7 +742,7 @@ s2 i Chaining score of the best secondary chain NM i Total number of mismatches and gaps in the alignment MD Z To generate the ref sequence in the alignment AS i DP alignment score -SA Z List of other supplementary alignments +SA Z List of other supplementary alignments (with approximate CIGAR strings) ms i DP score of the max scoring segment in the alignment nn i Number of ambiguous bases in the alignment ts A Transcript strand (splice mode only)