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commit eb7e9fdb8625225d7072b7ef599be9beafbc4021 Author: Afif Elghraoui <a...@ghraoui.name> Date: Wed Jul 29 23:45:30 2015 -0700 Finalize manpage for samtoh5 --- debian/samtoh5.1 | 71 +++++++++++++++++++++++++++----------------------------- 1 file changed, 34 insertions(+), 37 deletions(-) diff --git a/debian/samtoh5.1 b/debian/samtoh5.1 index 3c6b0a1..3880048 100644 --- a/debian/samtoh5.1 +++ b/debian/samtoh5.1 @@ -1,56 +1,53 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. .TH SAMTOH5 "1" "July 2015" "samtoh5 3ca7fe8" "User Commands" .SH NAME -samtoh5 \- description of program -.SH DESCRIPTION -samtoh5 Converts in.sam file to out.cmp.h5 file. -.PP -usage: samtoh5 in.sam reference.fasta out.cmp.h5 [options] -.IP -in.sam -.IP +samtoh5 \- convert a SAM file to cmp.h5 format +.SH SYNOPSIS +.B samtoh5 +.I in.sam +.I reference.fasta +.I out.cmp.h5 +.RI [ options ] +.SH OPTIONS +.TP +.I in.sam Input SAM file. -.IP -reference.fasta -.IP +.TP +.I reference.fasta Reference used to generate reads. -.IP -out.cmp.h5 -.IP +.TP +.I out.cmp.h5 Output cmp.h5 file. -.HP -\fB\-smrtTitle\fR -.IP +.TP +.B \-smrtTitle Use this option when converting alignments generated from reads -produced by the pls2fasta from bas.h5 files by parsing read -coordinates from the SMRT read title. The title is in the +produced by the +.BR pls2fasta (1) +from bas.h5 files by parsing read +coordinates from the SMRT read title. The title is in the format \fI\,/name/hole/coordinates\/\fP, where coordinates are in the format \ed+_\ed+, and represent the interval of the read that was aligned. -.HP -\fB\-readType\fR value -.IP +.TP +.BI \-readType \0value Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA' -.HP -\fB\-verbosity\fR value -.IP +.TP +.BI \-verbosity \0value Set desired verbosity. -.HP -\fB\-useShortRefName\fR -.IP -Use abbreviated reference names obtained from file.sam instead -of using full names from reference.fasta. -.HP -\fB\-copyQVs\fR -.IP +.TP +.B \-useShortRefName +Use abbreviated reference names obtained from \fIfile.sam\fR instead +of using full names from \fIreference.fasta\fR. +.TP +.B \-copyQVs Copy all QVs available in the SAM file into the cmp.h5 file. This includes things like InsertionQV and DeletionTag. -.IP +.SH NOTES Because SAM has optional tags that have different meanings in different programs, careful usage is required in order to have proper output. The "xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM -(blasr) it is defined as the start in the query sequence of the alignment. -When "\-smrtTitle" is specified, the xs tag is ignored, but when it is not +.RB ( blasr (1)) +it is defined as the start in the query sequence of the alignment. +When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not specified, the coordinates given by the xs and xe tags are used to define the interval of a read that is aligned. The CIGAR string is relative to this interval. -- 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