There is no XA equivalent in minimap2. I could add it, but this will take some time. For now, you can use --secondary=yes. It outputs secondary alignments. However, because the format is different, you can't simply adapt XA-aware tools to work with --secondary=yes output.

For tags, see the man page.

thank you. I missed the man page. XA would be useful, but it is not necessary. I'll leave this open, but feel free to close if you feel it's not of general interest.

@lh3 @brentp

test.zip

There are 2 alignment position in ref.3bp.in.fa for query_SE_150.fq.
one is full match. and another is with 3bp insert.

command line

# minimap2 --version
2.12-r847-dirty
#minimap2 -a -x sr --MD -t 40 -k15 -w1 -d ref.3bp.in.fa.sr.mmi ref.3bp.in.fa
#minimap2 -a -x sr --MD -t 40 -k15 -w1 --secondary=yes ref.3bp.in.fa.sr.mmi query_SE_150.fq

when 'default kmer size: 21; skip: 11', the score value is 141 vs 138.(OK)
when '-k15 -w3', the score value is 147 vs 143.(OK)
when '-k15 -w2', the score value is 148 vs 146.(OK)
when '-k15 -w1', the score value is 150 vs 150.(bug?)

checking score value by mm_select_sub function:

diff --git a/hit.c b/hit.c
index 92aa6b7..189b231 100644
--- a/hit.c
+++ b/hit.c
@@ -244,6 +244,7 @@ void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_,
                        if (p == i || r[i].inv) { // primary or inversion
                                r[k++] = r[i];
                        } else if ((r[i].score >= r[p].score * pri_ratio || r[i].score + min_diff >= r[p].score) && n_2nd < best_n) {
+                               fprintf(stderr,"DEBUG:%d\t%d\t%d\t%f\n",r[p].score,r[i].score,min_diff,pri_ratio);
                                if (!(r[i].qs == r[p].qs && r[i].qe == r[p].qe && r[i].rid == r[p].rid && r[i].rs == r[p].rs && r[i].re == r[p].re)) // not identical hits
                                        r[k++] = r[i], ++n_2nd;
                                else if (r[i].p) free(r[i].p);

@wangyugui Sorry that I have missed your question. Please create a new issue if you still have troubles.

@brentp I am afraid that I will decline this feature request. It seems not much needed by other users. Thanks for this anyway.