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Updated the manpage

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Heng Li
2021-11-18 17:28:31 -05:00
parent a3337c09f1
commit 736301fa6b
1 changed files with 15 additions and 4 deletions
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minimap2.html
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@@ -219,9 +219,15 @@ ignore minimizers occuring more than
<B>-U</B><I> INT1</I><B>[,</B><I>INT2</I><B>]</B> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Lower and upper bounds of k-mer occurrences [10,1000000]. The final k-mer occurrence threshold is
max{<I>INT1</I>, min{<I>INT2</I>, <B>-f</B>}}. This option prevents excessively small or large
<B>-f</B> estimated from the input reference. It deprecates
<B>-f</B> estimated from the input reference. Available since r1034 and deprecating
<B>--min-occ-floor</B> in earlier versions of minimap2.
</TD></TR>
<TR valign=top><TD colspan=2>
<B>--q-occ-frac</B><I> FLOAT</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Discard a query minimizer if its occurrence is higher than
<I>FLOAT</I> fraction of query minimizers and than the reference occurrence threshold
[0.01]. Set 0 to disable. Available since r1105.
</TD></TR>
<TR valign=top><TD width=10% nowrap>
<B>-e</B><I> INT</I> </TD><TD valign=bottom>
Sample a high-frequency minimizer every
@@ -492,6 +498,11 @@ alignment.
Skip alignment if the DP matrix size is above
<I>NUM</I>. Set 0 to disable [100m].
</TD></TR>
<TR valign=top><TD colspan=2>
<B>--cap-kalloc</B><I> NUM</I> </TD></TR><TR valign=top><TD width=10%>&nbsp;</TD><TD>
Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
<I>NUM</I>. Set 0 to disable [0].
</TD></TR>
<TR></TR></TABLE></BLOCKQUOTE>
<A name=7></A>
@@ -653,7 +664,7 @@ Long assembly to reference mapping
<TR valign=top><TD width=10% nowrap>
<B>splice</B> </TD><TD valign=bottom>
Long-read spliced alignment
(<B>-k15</B> <B>-w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0</B> <B>--splice-flank=yes</B>). In the splice mode, 1) long deletions are taken as introns and represented as
(<B>-k15</B> <B>-w5 --splice -g2k -G200k -A1 -B2 -O2,32 -E1,0 -b0 -C9 -z200 -ub --junc-bonus=9 --cap-sw-mem=0</B> <B>--splice-flank=yes</B>). In the splice mode, 1) long deletions are taken as introns and represented as
the
&#145;<B>N</B>&#146; CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the
@@ -666,7 +677,7 @@ Long-read splice alignment for PacBio CCS reads
<TR valign=top><TD width=10% nowrap>
<B>sr</B> </TD><TD valign=bottom>
Short single-end reads without splicing
(<B>-k21</B> <B>-w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -r100 -p.5 -N20 -f1000,5000 -n2 -m20</B> <B>-s40 -g100 -2K50m --heap-sort=yes</B> <B>--secondary=no</B>). </TD></TR>
(<B>-k21</B> <B>-w11 --sr --frag=yes -A2 -B8 -O12,32 -E2,1 -b0 -r100 -p.5 -N20 -f1000,5000 -n2 -m20</B> <B>-s40 -g100 -2K50m --heap-sort=yes</B> <B>--secondary=no</B>). </TD></TR>
<TR valign=top><TD width=10% nowrap>
<B>ava-pb</B> </TD><TD valign=bottom>
PacBio CLR all-vs-all overlap mapping
@@ -837,4 +848,4 @@ non-SSE2/NEON 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>minimap2-2.21 (r1071)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>6 July 2021</I></TD> </TR></TABLE></div></BODY></HTML>
<TABLE width=100%><TR> <TD width=33%><I>minimap2-2.23 (r1111)</I></TD> <TD width=33% align=center>minimap2 (1)</TD> <TD align=right width=33%><I>18 November 2021</I></TD> </TR></TABLE></div></BODY></HTML>