From dc37aee881dc613563e3a49042ef171b752a43e4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 21 Oct 2017 23:38:05 -0400 Subject: [PATCH] minor wording changes --- README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 44f97fe7..df628a4b 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ man ./minimap2.1 - [Map short accurate genomic reads](#short-genomic) - [Full genome/assembly alignment](#full-genome) - [Advanced features](#advanced) - - [Working CIGARs with >65535 operations in BAM](#long-cigar) + - [Working CIGARs with >65535 operations](#long-cigar) - [The cs optional tag](#cs) - [Evaluation scripts](#eval) - [Algorithm overview](#algo) @@ -179,13 +179,14 @@ according to the sequence divergence. ### Advanced features -#### Working CIGARs with >65535 operations in BAM +#### Working CIGARs with >65535 operations -At present, BAM does not work with CIGAR strings with >65535 operations. -However, aligning ultra-long nanopore reads with minimap2 may align ~1% of read -bases with long CIGARs beyond the capability of BAM. If you convert such SAM to -BAM, recent samtools will throw an error and abort. Older samtools and other -tools may even silently create corrupted and unreadable BAMs. +Due to a design flaw, BAM does not work with CIGAR strings with >65535 +operations (SAM and CRAM work). However, for ultra-long nanopore reads minimap2 +may align ~1% of read bases with long CIGARs beyond the capability of BAM. If +you convert such SAM/CRAM to BAM, recent samtools will throw an error and +abort. Older samtools and other tools may even silently create corrupted and +unreadable BAMs. To avoid this issue, you can add option `-L` at the minimap2 command line. This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR