update docs

Author: imsuneth

README.md

@@ -119,7 +119,7 @@ basic options:
 - See [how to consider inserted modified bases?](#enable-insertions)
 
 **Sample mods.tsv output**
-The output is ordered in the same as reads appear in the input BAM file, and for each read, entries are sorted by reference contig, reference position, strand, and modification code.
+The output is ordered in the same as the order the reads appear in the input BAM file, and for each read, entries are sorted by reference contig, reference position, strand, and modification code.
 ```bash
 ref_contig	ref_pos	strand	read_id	read_pos	mod_code	mod_prob
 chr22	19979864	+	m84088_230609_030819_s1/55512555/ccs	14	m	0.709804

docs/changes.md

@@ -12,4 +12,6 @@
 
 - For >=v0.5.0, when a context is provided (ex: -c h[CG]) option, we output modifications where the modified read base matches aligned reference base. However, when the context is * (ex: -c a[*]), this comparison is ignored and modifications at both matched and mismatched positions are output. Note that only the modified base is compared with reference base, not the whole context.
 
-- For >=v0.5.0, we print a warning if a certain modification and a context is untested.  For versions before this, only m[CG] for DNA (genome) and a[A] for transcriptome were tested.
+- For >=v0.5.0, we print a warning if a certain modification and a context is untested.  For versions before this, only m[CG] for DNA (genome) and a[A] for transcriptome were tested.
+
+- For <=v0.4.0, minimod view output was not properly sorted when using multiple threads. We have fixed it >=v0.5.0 and now view output is ordered in the same as the order the reads appear in the input BAM file, and for each read, entries are sorted by reference contig, reference position, strand, and modification code.