r151: documentations

minimap2.1

@@ -142,7 +142,7 @@ not using
 .BR -H )
 minus base-2 logarithm gap penalty. It is computed with dynamic programming.
 .TP
-.B -S
+.B -X
 Perform all-vs-all mapping. In this mode, if the query sequence name is
 lexicographically larger than the target sequence name, the hits between them
 will be suppressed; if the query sequence name is the same as the target name,
@@ -160,7 +160,9 @@ the secondary chain will not be outputted or extended with DP alignment later.
 .BI -N \ INT
 Output at most
 .I INT
-secondary alignments [5]
+secondary alignments [5]. This option has no effect when
+.B -X
+is applied.
 .TP
 .BI -D \ FLOAT
 Discard a chain if the fraction of matching bases over the length of
@@ -179,7 +181,7 @@ are:
 .RS
 .TP 8
 .B ava10k
-PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -Sw5 -p0 -m100 -D.05)
+PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05)
 .TP
 .B map10k
 PacBio/Oxford Nanopore read to reference mapping (-Hk19)
@@ -224,14 +226,24 @@ by default.
 Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
 .TP
 .BI -t \ INT
-Number of threads [3]. Minimap2 uses at most three threads when collecting
-minimizers on target sequences, and uses up to 
+Number of threads [3]. Minimap2 uses at most three threads when indexing target
+sequences, and uses up to
 .IR INT +1
 threads when mapping (the extra thread is for I/O, which is frequently idle and
 takes little CPU time).
 .TP
 .B -V
 Print version number to stdout
+.SS Miscellaneous options
+.TP 10
+.B --no-kalloc
+Use the libc default allocator instead of the kalloc thread-local allocator.
+This debugging option is mostly used with Valgrind to detect invalid memory
+accesses. Minimap2 runs slower with this option, especially in the
+multi-threading mode.
+.TP
+.B --print-qname
+Print query names to stderr, mostly to see which query is crashing minimap2.
 .SH OUTPUT FORMAT
 .PP
 Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by