fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-27 12:28:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

Use the full MIDNSHP=X string whenever printing CIGAR strings

Browse Source 
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.

It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
This commit is contained in:
John Marshall
2021-07-02 13:03:03 -04:00
committed by Heng Li
parent 459ce04c84
commit 177eef259d
6 changed files with 10 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files
misc/paftools.js
+3 -3
View File
@@ -1419,7 +1419,7 @@ function paf_view(args)
var s_ref = new Bytes(), s_qry = new Bytes(), s_mid = new Bytes(); // these are used to show padded alignment
var re_cs = /([:=\-\+\*])(\d+|[A-Za-z]+)/g;
var re_cg = /(\d+)([MIDNSH])/g;
var re_cg = /(\d+)([MIDNSHP=X])/g;
var buf = new Bytes();
var file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
@@ -1899,7 +1899,7 @@ function paf_splice2bed(args)
a.length = 0;
}
var re = /(\d+)([MIDNSH])/g;
var re = /(\d+)([MIDNSHP=X])/g;
var c, fmt = "bed", fn_name_conv = null, keep_multi = false;
while ((c = getopt(args, "f:n:m")) != null) {
if (c == 'f') fmt = getopt.arg;
@@ -2369,7 +2369,7 @@ function paf_junceval(args)
file = getopt.ind+1 >= args.length || args[getopt.ind+1] == '-'? new File() : new File(args[getopt.ind+1]);
var last_qname = null;
var re_cigar = /(\d+)([MIDNSHX=])/g;
var re_cigar = /(\d+)([MIDNSHP=X])/g;
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
var ctg_name = null, cigar = null, pos = null, qname = t[0];