This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository blasr.
commit 4edf806d575d743d82f3c25c7d21d0a9ef8677a7 Author: Afif Elghraoui <a...@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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit