forked from pervouchine/bam2ssj
-
Notifications
You must be signed in to change notification settings - Fork 0
/
VERSION
23 lines (19 loc) · 1.1 KB
/
VERSION
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
v1.3, 2012/07/15
1) strands are treated separately (separate pointers)
2) bug with over-writibg the value of end and other_end fixed
3) summary became side-specific
4) added: GPL
v1.4 1) read strandness is specified in the command line; switch_reads deprecated
2) report read statistics on rd1/rd2 and +/- strand
3) index file is not needed, removed loading bai file
4) check whether the BAM file was sorted and if not then exit(1)
5) support reads with more than one N in cigar (keep counting when read spans over more than one junction)
6) updated statistics on read counts
7) soft and hard clipping + padding operations added
v1.5 1) if stranded AND (read is both read1 and read2 OR read is neither read1 nor read2) then skip
2) if not stranded then report only one (correct) strand in both output file and log file
3) min_lemgth and max_length added as command line options
v1.6 1) added example.mk, it downloads gencode v10 and one of the bam files, then runs bam2ssj
2) cleaned up the readme file
v1.7 1) added contraint on flagged reads
2) important: added margin for supporting and covering reads