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Description
See below.
It looks like the pointer doesn't know where to stop; it gives the correct result up to {cigar = SoftClip, length = 23}
import qualified Bio.SamTools.BamIndex as Bai
import qualified Bio.SamTools.Bam as Bam
*Lib Bam Bai Bam> let xs' = Bai.withIndex "113.bam" (\x -> Bai.readBamRegion x 0 (1, 3))
*Lib Bam Bai Bam> xs <- xs'
*Lib Bam Bai Bam> let b1 = head xs
*Lib Bam Bai Bam> b1
M02261:12:000000000-A6FJ2:1:1101:15738:2449 97 H3N2/CY074922/Managua/2010/PB2_1 1 60 15S213M23S = 2079 2310 AGCAAAAGCAGGCCAATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATCACTGCTGACAAAAGGGTAACAGAAATGGTTTTGAAGACCCAGATGAAAGCACA A>1A@@B1?1F?1AAFFGB3GGBFDBFHCGGHCFHFHHHFGHC0G0GEHFFGEEFBGHGHFFEEGGEEEG0FECEHGGGCEGFHBFFFHHHHHHFGHAGF11FDGHHHGHHHEHHHHHEFFHHFFHFHEHHGCFCGC<BCGGFHEFHFHEFFHE?-<AACHHHHHBDCF0DB0CGHHC00:CFCGC0GBCBC:CGB0;GB900BFF/9CBAFB?.:/0;BFFFBFB00;9F?FFB/-;--A/B//B/9:-9 NM:i:0 AS:i:213 XS:i:0 RG:Z:MiSeq
*Lib Bam Bai Bam> Bam.cigars b1
[Cigar {cigar = SoftClip, length = 15},Cigar {cigar = Match, length = 213},Cigar {cigar = SoftClip, length = 23},Cigar {cigar = SoftClip, length = 21041681},Cigar {cigar = Ins, length = 17966146},*** Exception: ./Data/Vector/Generic.hs:245 ((!)): index out of bounds (8,7)
CallStack (from HasCallStack):
error, called at ./Data/Vector/Internal/Check.hs:87:5 in vector-0.12.0.1-81HFvG2McTgAiNXCyGXulK:Data.Vector.Internal.CheckI made sure to index and sort the BAM using samtools version 0.1.13.
samtools-0.1.13$ ./samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.13 (r926:134)
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