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brittneybrinsfield / pysam

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Support for FZ (flow intensities) field with B (array) of small ints #81

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Feature request for support for FZ (flow intensity) field with B (array) and S 
(small int) for an optional field.

Request that pysam returns an appropriate array when requesting this field.

Underlying samtools requirement is 0.1.18, (which was just incorporated into 
the 0.6 release).

Request support for LINUX platform.

Please provide any additional information below.
An example BAM record with flow intensities:

QW85I:468:729   0   chr1    156268499   63  140M15H *   0   0   GTCCAGTCTCCTGTAATTCTTGGGCTTGACTA
GGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAA
CATTGGAAGATGGCACAAACAATTCAGT    >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>
>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>5
88-1.19<=   RG:Z:QW85I  PG:Z:tmap   MD:Z:140    NM:i:0  AS:i:140    FZ:B:S,100,1,91,0,7,101,
0,201,96,204,0,0,87,109,0,7,97,112,1,12,78,197,0,7,100,95,101,202,0,6,0,1,186,0,
84,0,244,0,0,324,0,107,195,101,113,0,102,0,104,3,0,101,1,0,212,6,0,0,1,0,74,1,11
,0,196,2,197,103,0,108,98,2,7,0,1,2,194,0,180,0,108,0,203,104,16,5,205,0,0,0,1,1
,100,98,0,0,204,6,0,79,0,0,101,7,109,90,265,1,27,10,109,102,9,0,292,0,110,0,0,10
2,112,0,0,84,100,103,2,81,126,0,2,90,0,15,96,15,1,0,2,0,107,92,0,0,101,3,98,15,1
02,13,116,116,90,93,198,0,0,0,199,92,26,495,100,5,0,100,5,209,0,92,107,90,0,0,0,
0,109,194,7,94,200,0,40,197,0,11,0,0,112,110,6,4,200,28,0,196,0,203,1,129,0,0,1,
0,94,0,1,0,107,5,201,3,3,100,0,121,0,7,0,1,105,306,3,86,8,183,0,12,163,17,83,22,
0,0,1,8,109,103,0,0,295,0,200,16,172,3,16,182,3,11,0,0,223,111,103,0,5,225,0,95 
XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1  XE:i:0

Original issue reported on code.google.com by efts...@gmail.com on 7 Dec 2011 at 5:39

GoogleCodeExporter commented 9 years ago 
Done, sorry this took so long. 

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 21 Nov 2012 at 12:54

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
This is great!  We saw the difficulty of this because it seemed 
at the time that samtools C api lacked good support for binary data formats 
(:B:).

Original comment by efts...@gmail.com on 26 Nov 2012 at 9:07