From a05edfa5ece3588030b8035d0fffbbd69b390fd9 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 7 Aug 2021 10:38:48 -0400 Subject: [PATCH] a different ending sentence --- misc/paftools.js | 2 +- tex/mm2-update.tex | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/misc/paftools.js b/misc/paftools.js index 656ec38..11d7722 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -1084,7 +1084,7 @@ function paf_stat(args) } if (NM != null) { var tmp = NM - n_gap_all - nn; - if (tmp < 0) warn("WARNING: NM is smaller than the number of gaps at line " + lineno); + if (tmp < 0 && nn == 0) warn("WARNING: NM is smaller than the number of gaps at line " + lineno + ": NM=" + NM + ", nn=" + nn + ", G=" + n_gap_all); if (tmp < 0) tmp = 0; n_sub += tmp; } diff --git a/tex/mm2-update.tex b/tex/mm2-update.tex index cd27711..7c596ba 100644 --- a/tex/mm2-update.tex +++ b/tex/mm2-update.tex @@ -211,9 +211,8 @@ not report the numbers. Minimap2 spends most computing time on base alignment. As recent improvements in v2.22 incur little additional computing and do not change the base alignment algorithm, the new version has similar performance to older verions. It is -consistently faster than Winnowmap2 by several times. Our simple heuristics can -be as effective as more complex solutions on real data and may help the -development of future sequence aligners. +consistently faster than Winnowmap2 by several times. Sometimes simple +heuristics can be as effective as more sophisticated yet slower solutions. \section*{Acknowledgements} We thank Arang Rhie and Chirag Jain for providing motivating examples where