updated manpage

minimap2.html

@@ -61,7 +61,7 @@ p {
     text-align: justify;
 }
 </style>
-<TITLE>Manual Page - minimap2(1)</TITLE>
+<TITLE>minimap2.1</TITLE>
 </HEAD>
 <BODY bgcolor=#F0F0F0 text=#000000 link=#0000ff vlink=#C000C0 alink=#ff0000><div id="wrap"><A NAME=top></A>
 <CENTER>
@@ -172,6 +172,13 @@ Load at most
 <I>NUM</I> may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
 multi-part index.
 </TD></TR>
+<TR valign=top><TD colspan=2>
+<B>--idx-no-seq</B> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
+Don&#146;t store target sequences in the index. It saves disk space and memory but
+the index generated with this option will not work with
+<B>-a</B> or
+<B>-c</B>. When base-level alignment is not requested, this option is automatically applied.
+</TD></TR>
 <TR valign=top><TD width=10% nowrap>
 <B>-d</B><I> FILE</I> </TD><TD valign=bottom>
 Save the minimizer index of
@@ -344,6 +351,15 @@ accuracy by several percents, so it is applied by default with
 on SIRV data, please add
 <B>--splice-flank=no</B> to the command line.
 </TD></TR>
+<TR valign=top><TD colspan=2>
+<B>--end-seed-pen</B><I> INT</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
+Drop a terminal anchor if
+<I>s</I>&lt;log(<I>g</I>)+<I>INT</I>, where
+<I>s</I> is the local alignment score around the anchor and
+<I>g</I> the length of the terminal gap in the chain. This option is only effective
+with
+<B>--splice</B>. It helps to avoid tiny terminal exons. [6]
+</TD></TR>
 <TR></TR></TABLE></BLOCKQUOTE>
 <A name=7></A>
 
@@ -563,7 +579,7 @@ the SAM-like typed key-value format. Minimap2 may output the following tags:
 <TD align=center><B>Tag</B></TD><TD align=center><B>Type</B></TD><TD align=center><B>Description</B></TD></TR>
 <TR></TR><TR></TR>
 <TR valign=top>
-<TD align=right>tp</TD><TD align=center>A</TD><TD>Type of aln: P/primary, S/secondary and I/inversion</TD></TR>
+<TD align=right>tp</TD><TD align=center>A</TD><TD>Type of aln: P/primary, S/secondary and I,i/inversion</TD></TR>
 <TR valign=top>
 <TD align=right>cm</TD><TD align=center>i</TD><TD>Number of minimizers on the chain</TD></TR>
 <TR valign=top>
@@ -640,4 +656,4 @@ non-SSE2 support, but it would make minimap2 slower by several times.
 miniasm(1), minimap(1), bwa(1).
 </BLOCKQUOTE>
 <P><HR>
-<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.5 (r572)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>11 November 2017</I></TD> </TR></TABLE></div></BODY></HTML>
+<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.6 (r623)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>12 December 2017</I></TD> </TR></TABLE></div></BODY></HTML>