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removed unnecessary empty lines 

On linux, these empty lines count.
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Heng Li 2017-07-01 11:31:32 -04:00
parent b883d132e2
commit cb6c277c62
1 changed files with 0 additions and 13 deletions
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minimap2.1
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@ -64,7 +64,6 @@ ava10k
> >
.I output.paf .I output.paf
.RE .RE
.SH DESCRIPTION .SH DESCRIPTION
.PP .PP
Minimap2 is a fast sequence mapping and alignment program that can find Minimap2 is a fast sequence mapping and alignment program that can find
@ -73,11 +72,8 @@ reference genome optionally with detailed alignment (i.e. CIGAR). At present,
it works efficiently with query sequences from a few kilobases to ~100 it works efficiently with query sequences from a few kilobases to ~100
megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
SAM format. SAM format.
.SH OPTIONS .SH OPTIONS
.SS Indexing options .SS Indexing options
.TP 10 .TP 10
.BI -k \ INT .BI -k \ INT
Minimizer k-mer length [17] Minimizer k-mer length [17]
@ -111,9 +107,7 @@ Save the minimizer index of
to to
.I FILE .I FILE
[no dump] [no dump]
.SS Mapping options .SS Mapping options
.TP 10 .TP 10
.BI -f \ FLOAT .BI -f \ FLOAT
Ignore top Ignore top
@ -183,9 +177,7 @@ PacBio/Oxford Nanopore read to reference mapping (-Hk19)
.B asm1m .B asm1m
Long assembly to reference mapping (-k19 -w19) Long assembly to reference mapping (-k19 -w19)
.RE .RE
.SS Alignment options .SS Alignment options
.TP 10 .TP 10
.BI -A \ INT .BI -A \ INT
Matching score [1] Matching score [1]
@ -212,9 +204,7 @@ the contiguity of the alignment at the cost of poor alignment in the middle
Minimal peak DP alignment score to output [40]. The peak score is computed from Minimal peak DP alignment score to output [40]. The peak score is computed from
the final CIGAR. It is the score of the max scoring segment in the alignment the final CIGAR. It is the score of the max scoring segment in the alignment
and may be different from the total alignment score. and may be different from the total alignment score.
.SS Input/output options .SS Input/output options
.TP 10 .TP 10
.B -b .B -b
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
@ -232,7 +222,6 @@ takes little CPU time).
.TP .TP
.B -V .B -V
Print version number to stdout Print version number to stdout
.SH OUTPUT FORMAT .SH OUTPUT FORMAT
.PP .PP
Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
@ -257,7 +246,6 @@ _
11 int Number bases, including gaps, in the mapping 11 int Number bases, including gaps, in the mapping
12 int Mapping quality (0-255 with 255 for missing) 12 int Mapping quality (0-255 with 255 for missing)
.TE .TE
.PP .PP
When alignment is available, column 11 gives the total number of sequence When alignment is available, column 11 gives the total number of sequence
matches, mismatches and gaps in the alignment; column 10 divided by column 11 matches, mismatches and gaps in the alignment; column 10 divided by column 11
@ -279,7 +267,6 @@ ms i DP score of the max scoring segment in the alignment
nn i Number of ambiguous bases in the alignment nn i Number of ambiguous bases in the alignment
cg Z CIGAR string (only in PAF) cg Z CIGAR string (only in PAF)
.TE .TE
.SH SEE ALSO .SH SEE ALSO
.PP .PP
miniasm(1), minimap(1), bwa(1). miniasm(1), minimap(1), bwa(1).