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vd4mmind / pysam

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truncated read groups #132

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
-bash-3.2$ ll
total 8324
-rw-r--r-- 1 ccri0039 PCCR0004 7617577 Jul 15 10:22 in.bam
-rw-r--r-- 1 ccri0039 PCCR0004  901064 Jul 15 11:08 in.bam.bai
-rwxr-xr-x 1 ccri0039 PCCR0004     443 Jul 15 11:23 rg.py
-bash-3.2$ ./rg.py 
-bash-3.2$ samtools view -h out.bam > test.sam
-bash-3.2$ samtools view -Sbo test.bam test.sam
[samopen] SAM header is present: 25 sequences.
Parse error at line 3494: missing colon in auxiliary data
Aborted
-bash-3.2$ sed -n 3494p test.sam
20FUKAAXX100202:6:28:9089:10995 99      chr20   120032  9       101M    =       
120307  376     
TAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAA
AAATAAAGAAAAAAGAATTTT   
8<35.<;9;>>C@BACD@BDACADFAFCACFBEEDDEBFDBEEEFEDDCCFCEDFDEEEECFFEEEFCEEEEEEFEFCFG
GGDDDDDCGGBDDDCDCCDC=     XT:A:R  NM:i:71 SM:i:0  AM:i:0  X0:i:2  X1:i:1  
XM:i:5  XO:i:0  XG:i:0  
MD:Z:0A0C1A0T1G1C0T0A0A1C0C0A0A0G0C0A0G1A0G1A1G2G0T0T0C0A0G1A0C0T0T0G0A0A0G1C1A0
G0T0C3T0A1G0A0A0T0T0A0A0C0C1A0G0T0C0A0G1C1A3T1A1G1A5T0T0T0T0A0A0A0A0      
XA:Z:chr20,+120030,101M,5;chr20,+120030,93M2I6M,2;chr20,+120030,94M1I6M,3;RG:Z:t
est_chrt@
-bash-3.2$

What is the expected output? What do you see instead?
RG in out.bam should be "test_chrtwenty", but is truncated in the actual output.

What version of the product are you using? On what operating system?
Python 2.7.5
pysam-0.7.4

Please provide any additional information below.
pysam-0.6 does not have this issue
I think this is probably the same as issue 115, but I created a new issue so I 
could attach files (didn't know how to attach to the existing issue).

Original issue reported on code.google.com by fit...@gmail.com on 15 Jul 2013 at 3:57

Attachments:

GoogleCodeExporter commented 8 years ago 
Looks like this is a duplicate of issue 129. I can't say for sure, but I think 
issue 115 probably is as well.

I verified that my problem is solved if I use the trunk version from the 
repository (rather than the 0.7.4 release version).

Original comment by fit...@gmail.com on 16 Jul 2013 at 6:16

GoogleCodeExporter commented 8 years ago 
Thanks, it does seem to work for me as well now.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 18 Sep 2013 at 6:50