09-28-2012
mapped reads using samtools flagstat options
Hey guys,
Does anyone know how to calculate total number of mapped reads for a certain region of a bam file using samtools flagstat?
I know to use flagstat for the whole bam file. but for a specific region of it... is there an option?
Tnx
---------- Post updated at 12:27 PM ---------- Previous update was at 05:50 AM ----------
Oh I just realized that the tool was "samtools view" which is able to calculate the mapped reads of a certain region of a given bam file.
But I don't know how to do it yet; and which options should I use.
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LEARN ABOUT DEBIAN
dbs-edit-patch
DBS-EDIT-PATCH(1) Debian Build System DBS-EDIT-PATCH(1)
NAME
dbs-edit-patch - Edit a DBS patch
SYNOPSIS
dbs-edit-patch [options] patch
dbs-edit-patch -h|--help
DESCRIPTION
dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format.
WARNING
dbs is deprecated, please switch to the `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb-
Src3.0#FAQ for a short guide how to do it.
OPTIONS
-h, --help
Show summary of options.
-t dir, --tmpdir=dir
Directory for the temporary files, default is /tmp or if set $TMP.
-s dir, --sourcedir=dir
Top level directory of the debian-package source-tree, default is the present working directory.
-P dir, --sourcepatchdir=dir
Directory containing upstream patches.
-T dir, --sourcetardir=dir
Directory containing the upstream tarball.
-p level, --strip=level
Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0.
ENVIRONMENT VARIABLES
TMP Sets the directory for the temporary files, can be overridden with -t dir.
debian/vars
dbs-edit-patch will automatically use variables defined in the optional debian/vars file.
When a file debian/vars.in exists and debian/vars either does not exist or is older than any of the following files: debian/vars.in,
debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command
make -f debian/rules -W debian/vars.in debian/vars
EXAMPLES
Edit the 021_debian patch of Heimdal:
~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian
Extracting source heimdal-0.3d.tar.gz ... successful.
Applying patch 001_replay ... successful.
etc.
Copying heimdal-0.3d to heimdal-0.3d-old ... successful.
Applying patch 021_debian ... successful.
Edit files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired,
and finally execute /tmp/021_debian/dbs-update-patch to save the results.
Technical note: dbs-edit-patch extracts all patches before 021_debian into /tmp/021_debian/heimdal-0.3d, copies the result to
/tmp/021_debian/heimdal-0.3d-old, and applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create
the diff between the old and new directories:
~/heimdal-0.3d> ls -la /tmp/021_debian
total 12
-rwxr-xr-x 1 bam users 112 Jan 31 13:31 dbs-update-patch*
-rw-r--r-- 1 bam users 0 Jan 31 13:31 patch-description
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d/
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d-old/
drwxr-xr-x 5 bam users 4096 Jan 31 13:31 .stampdir/
~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch
#!/bin/sh -e
cd "/tmp/021_debian"
HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks"
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff
find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm
find -name "*~" -print0 | xargs -0 --no-run-if-empty rm
: > new_patch
test ! -e patch-description || cp patch-description new_patch
diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1
mv new_patch /usr/src/heimdal/debian/patches/021_debian
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff
SEE ALSO
diff(1), dbs(7), /usr/share/doc/dbs/
AUTHOR
DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by Brian May. This manpage was generated by
Andreas Metzler and modified by Robert Luberda.
Debian February 15th, 2011 DBS-EDIT-PATCH(1)