[med-svn] [blasr] 01/05: Finalize blasr man page

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
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commit 4edf806d575d743d82f3c25c7d21d0a9ef8677a7
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Jul 30 21:46:38 2015 -0700

    Finalize blasr man page
---
 debian/blasr.1 | 120 +++++++++++++++++++++++++--------------------------------
 1 file changed, 53 insertions(+), 67 deletions(-)

diff --git a/debian/blasr.1 b/debian/blasr.1
index 015be46..df93532 100644
--- a/debian/blasr.1
+++ b/debian/blasr.1
@@ -311,7 +311,7 @@ is not as exhaustive as the default, but is much faster.
 \fB\-aggressiveIntervalCut\fR (false)
 Agreesively filter out non-promising alignment candidates, if there
 exists at least one promising candidate. If this option is turned on,
-\fBblasr\fI is likely to ignore short alignments of ALU elements.
+\fBblasr\fR is likely to ignore short alignments of ALU elements.
 .TP
 \fB\-fastSDP\fR (false)
 Use a fast heuristic algorithm to speed up sparse dynamic programming.
@@ -328,105 +328,91 @@ rather than mapping sensitivity itself.
 \fB\-scoreMatrix\fI score matrix string
 Specify an alternative score matrix for scoring fasta reads.
 The matrix is in the format
-.IP
-ACGTN
-.IP
-A abcde
-C fghij
-G klmno
-T pqrst
-N uvwxy . The values a...y should be input as a quoted space separated
-.IP
-string: "a b c ... y". Lower scores are better, so matches should be less
-than mismatches e.g. a,g,m,s = \fB\-5\fR (match), mismatch = 6.
-.HP
-\fB\-affineOpen\fR value (10)
-.IP
+.TS
+;
+L L L L L L .
+  A C G T N
+A a b c d e
+C f g h i j
+G k l m n o
+T p q r s t
+N u v w x y
+.TE
+
+The values a...y should be input as a quoted space separated
+string: "a b c ... y". Lowerf scores are better, so matches should be less
+than mismatches e.g. a,g,m,s = \-5 (match), mismatch = 6.
+.TP
+\fB\-affineOpen\fI value\fR (10)
 Set the penalty for opening an affine alignment.
-.HP
-\fB\-affineExtend\fR a (0)
-.IP
+.TP
+\fB\-affineExtend\fI a \fR(0)
 Change affine (extension) gap penalty. Lower value allows more gaps.
 .RE
 .B Options for overlap/dynamic programming alignments and pairwise overlap for de novo assembly.
 .RS
-.HP
+.TP
 \fB\-useQuality\fR (false)
-.IP
 Use substitution/insertion/deletion/merge quality values to score gap and
-mismatch penalties in pairwise alignments.  Because the insertion and deletion
+mismatch penalties in pairwise alignments. Because the insertion and deletion
 rates are much higher than substitution, this will make many alignments
-favor an insertion/deletion over a substitution.  Naive consensus calling methods
+favor an insertion/deletion over a substitution.nNaive consensus calling methods
 will then often miss substitution polymorphisms. This option should be
-used when calling consensus using the Quiver method.  Furthermore, when
+used when calling consensus using the Quiver method. Furthermore, when
 not using quality values to score alignments, there will be a lower consensus
 accuracy in homolymer regions.
-.HP
+.TP
 \fB\-affineAlign\fR (false)
-.IP
 Refine alignment using affine guided align.
 .RE
 .B Options for filtering reads and alignments
 .RS
-.HP
-\fB\-minReadLength\fR l(50)
-.IP
-Skip reads that have a full length less than l. Subreads may be shorter.
-.HP
-\fB\-minSubreadLength\fR l(0)
-.IP
-Do not align subreads of length less than l.
-.HP
-\fB\-minRawSubreadScore\fR m(0)
-.IP
-Do not align subreads whose quality score in region table is less than m (quality scores should be in range [0, 1000]).
-.HP
-\fB\-maxScore\fR m(\fB\-200\fR)
-.IP
+.TP
+\fB\-minReadLength\fI l\fR (50)
+Skip reads that have a full length less than \fIl\fR. Subreads may be shorter.
+.TP
+\fB\-minSubreadLength \fIl \fR(0)
+Do not align subreads of length less than \fIl\fR.
+.TP
+\fB\-minRawSubreadScore \fIm \fR(0)
+Do not align subreads whose quality score in region table is less than \fIm\fR
+(quality scores should be in range [0, 1000]).
+.TP
+\fB\-maxScore\fI m \fR(\-200)
 Maximum score to output (high is bad, negative good).
-.HP
+.TP
 \fB\-minAlnLength\fR
-.IP
 (0) Report alignments only if their lengths are greater than minAlnLength.
 .HP
 \fB\-minPctSimilarity\fR
-.IP
 (0) Report alignments only if their percentage similairty is greater than minPctSimilarity.
-.HP
+.TP
 \fB\-minPctAccuracy\fR
-.IP
 (0) Report alignments only if their percentage accuray is greater than minAccuracy.
 .RE
 .B Options for parallel alignment
 .RS
-.HP
-\fB\-nproc\fR N (1)
 .TP
-Align using N processes.
-All large data structures such as the suffix array and
-.IP
-tuple count table are shared.
-.HP
-\fB\-start\fR S (0)
-.IP
-Index of the first read to begin aligning. This is useful when multiple instances
-are running on the same data, for example when on a multi\-rack cluster.
-.HP
-\fB\-stride\fR S (1)
-.IP
-Align one read every 'S' reads.
+\fB\-nproc\fI N \fR(1)
+Align using \fIN\fR processes. All large data structures such as the suffix array and tuple count table are shared.
+.TP
+\fB\-start\fI S \fR(0)
+Index of the first read to begin aligning.
+This is useful when multiple instances are running on the same data,
+for example when on a multi-rack cluster.
+.TP
+\fB\-stride\fI S \fR(1)
+Align one read every \fIS\fR reads.
 .RE
 .B Options for subsampling reads.
 .RS
-.HP
+.TP
 \fB\-subsample\fR (0)
-.IP
 Proportion of reads to randomly subsample (expressed as a decimal) and align.
-.HP
-\fB\-holeNumbers\fR LIST
-.IP
-When specified, only align reads whose ZMW hole numbers are in LIST.
-LIST is a comma\-delimited string of ranges, such as '1,2,3,10\-13'.
+.TP
+\fB\-holeNumbers\fI LIST
+When specified, only align reads whose ZMW hole numbers are in \fILIST\fR.
+\fILIST\fR is a comma-delimited string of ranges, such as '1,2,3,10\-13'.
 This option only works when reads are in bam, bax.h5 or plx.h5 format.
 .RE
 .TP

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