note on long cigar in README

README.md

@@ -34,6 +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)
     - [The cs optional tag](#cs)
     - [Evaluation scripts](#eval)
   - [Algorithm overview](#algo)
@@ -178,6 +179,26 @@ according to the sequence divergence.
 
 ### <a name="advanced"></a>Advanced features
 
+#### <a name="long-cigar"></a>Working CIGARs with >65535 operations in BAM
+
+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.
+
+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
+at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and
+sorting) still work with such BAM records; tools that read CIGAR will
+effectively ignore these records. I have pull requests to the SAM spec, htslib,
+htsjdk, bedtools2, Rsamtools and igv.js. If they are accepted, future versions
+of these tools will seamlessly recognize long-cigar records generated by option
+`-L`.
+
+In summary, if you work with ultra-long reads and use tools that only process
+BAM files, please add option `-L`.
+
 #### <a name="cs"></a>The cs optional tag
 
 The `cs` SAM/PAF tag encodes bases at mismatches and INDELs. It matches regular