From 25b2ae15dc3a74aa4a4c8ff37e35ebd9f30f0119 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Tue, 1 Mar 2022 00:12:53 +0000
Subject: [PATCH] Bump version

---
 CHANGELOG.md         |  5 +++++
 README.md            | 14 ++++++++------
 modbampy/__init__.py |  5 ++---
 src/version.h        |  2 +-
 4 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 507d09e..25f2905 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.5.0]
+### Changed
+- Decouple file opening from read iteration.
+- Move Python pileup function to method of ModBam class.
+
 ## [v0.4.6]
 ### Changed
 - Reworked compilation to remove argparser from Python module.
diff --git a/README.md b/README.md
index 1745dce..7b25b7e 100644
--- a/README.md
+++ b/README.md
@@ -148,9 +148,9 @@ over reads in a BAM file and report modification sites:
 
 ```
 from modbampy import ModBam
-with ModBam(args.bam, args.chrom, args.start, args.end) as bam:
+with ModBam(args.bam) as bam:
     for read in bam.reads():
-        for pos_mod in read.mod_sites():
+        for pos_mod in read.mod_sites(args.chrom, args.start, args.end):
             print(*pos_mod)
 ```
 
@@ -165,13 +165,15 @@ Each line of the above reports the
 * modified base,
 * modified-base score (scaled to 0-255).
 
-A second function is provided which mimics the couting procedure implemented in
+A second method is provided which mimics the couting procedure implemented in
 `modbam2bed`:
 
 ```
-positions, counts = pileup(
-    bam, chrom, start, end,
-    low_threshold=0.33, high_threshold=0.66, mod_base="m")
+from modbampy import ModBam
+with ModBam(args.bam) as bam:
+    positions, counts = bam.pileup(
+        args.chrom, args.start, args.end
+        low_threshold=0.33, high_threshold=0.66, mod_base="m")
 ```
 
 The result is two [numpy](https://numpy.org/) arrays. The first indicates the reference
diff --git a/modbampy/__init__.py b/modbampy/__init__.py
index 9b6eb85..4030447 100644
--- a/modbampy/__init__.py
+++ b/modbampy/__init__.py
@@ -8,7 +8,7 @@
 import libmodbampy
 
 # remember to bump version in src/version.h too
-__version__ = "0.4.6"
+__version__ = "0.5.0"
 ffi = libmodbampy.ffi
 libbam = libmodbampy.lib
 
@@ -40,8 +40,7 @@ def _tidy_args(read_group, tag_name, tag_value):
 class ModBam:
     """A minimal class to iterate over a bam."""
 
-    def __init__(
-            self, bam, read_group=None, tag_name=None, tag_value=None):
+    def __init__(self, bam):
         """Open a BAM file.
 
         :param bam: BAM file to open.
diff --git a/src/version.h b/src/version.h
index 9d3528a..1ac009d 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,2 +1,2 @@
 // remember to bump version in modbampy/__init__.py too
-const char *argp_program_version = "0.4.6";
+const char *argp_program_version = "0.5.0";