From 44eef16502ffb5f7faf45fc4a65da906418b3166 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Karel=20B=C5=99inda?= Date: Mon, 26 Feb 2018 17:55:52 -0500 Subject: [PATCH] Add chr1/2 examples + update version --- README.rst | 4 +++- samsift/version.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 6fc77bf..1d782d4 100644 --- a/README.rst +++ b/README.rst @@ -43,6 +43,8 @@ Getting started samsift -i tests/test.bam -f 'random.random()<0.25' -0 'random.seed(42)' # filtering: keep only alignments of reads specified in tests/qnames.txt samsift -i tests/test.bam -0 'q=open("tests/qnames.txt").read().splitlines()' -f 'QNAME in q' + # filtering: keep only first 5000 reads from chr1 and 5000 reads from chr2 + samsift -i tests/test.bam -0 'c={"chr1":5000,"chr2":5000}' -f 'c[RNAME]>0' -c 'c[RNAME]-=1' -m nonstop-remove # tagging: add tags 'ln' with sequence length and 'ab' with average base quality samsift -i tests/test.bam -c 'ln=len(SEQ);ab=1.0*sum(QUALa)/ln' # tagging: add a tag 'ii' with the number of the current alignment @@ -91,7 +93,7 @@ Command-line parameters .. code-block:: Program: samsift (advanced filtering and tagging of SAM/BAM alignments using Python expressions) - Version: 0.2.4 + Version: 0.2.5 Author: Karel Brinda Usage: samsift.py [-i FILE] [-o FILE] [-f PY_EXPR] [-c PY_CODE] [-m STR] diff --git a/samsift/version.py b/samsift/version.py index 43ec9c8..fbb8e30 100644 --- a/samsift/version.py +++ b/samsift/version.py @@ -1 +1 @@ -VERSION="0.2.4" \ No newline at end of file +VERSION="0.2.5" \ No newline at end of file