P CIGAR operator causes mpileup to stutter

Reproduce the issue with the provided c1#pad1.sam input and the samtools mpileup command. Trace how mpileup handles P CIGAR operators, then verify that position 5 reports the expected insertion strings without skipped or duplicated bases.

When given a BAM file using the P operator, mpileup can sometimes skip bases and duplicate others. Additionally there is no way to actually use the P operator properly, to know which bases align with which in an insertion region, but that is a different fault and a fundamental flaw in the output format.

An example:

@SQ SN:c1 LN:10
s0a 0 c1 1 0 10M * 0 0 AACCGCGGTT *
s0b 0 c1 1 0 10M * 0 0 AACCGCGGTT *
s0c 0 c1 1 0 10M * 0 0 AACCGCGGTT *
s1 0 c1 1 0 5M6I5M * 0 0 AACCGGTTAACCGGTT *
s2 0 c1 1 0 5M1P4I1P5M * 0 0 AACCGTTAACGGTT *
s3 0 c1 1 0 5M3I3P5M * 0 0 AACCGGTTCGGTT *
s4 0 c1 1 0 5M3P3I5M * 0 0 AACCGAACCGGTT *
s5 0 c1 1 0 4M1D2P2I2P1D4M * 0 0 AACCTAGGTT *
s6 0 c1 1 0 2M3D6I3D2M * 0 0 AAGTTAACTT *

jkb@seq3a[work/samtools...] ./samtools mpileup c1#pad1.bam
[mpileup] 1 samples in 1 input files
Set max per-file depth to 8000
c1 1 N 9 ^!A^!A^!A^!A^!A^!A^!A^!A^!A ~~~~~~~~~
c1 2 N 9 AAAAAAAAA-3NNN ~~~~~~~~~
c1 3 N 9 CCCCCCCC* ~~~~~~~~~
c1 4 N 9 CCCCCCCC-1N* ~~~~~~~~~
c1 5 N 9 GGGG+6GTTAACG+4TTAAG+3GTTG+3AAC_+2AG_+6TTAACT ~~~~~~~~~
c1 6 N 9 CCCCCCC** ~~~~~~~~~
c1 7 N 9 GGGGGGGG* ~~~~~~~~~
c1 8 N 9 GGGGGGGG* ~~~~~~~~~
c1 9 N 9 TTTTTTTTT ~~~~~~~~~
c1 10 N 9 T$T$T$T$T$T$T$T$T$ ~~~~~~~~~

Note that position 5 should end +2TA+6GTTAAC

Uuencoded SAM file to demonstrate the problem. (It's also c1#pad1.sam)

begin 644 -
M0%-1"5-..F,Q"4Q..C$P"G,P80DP"6,Q"3$),`DQ,$T)*@DP"3`)04%#0T=#
M1T=45`DJ"G,P8@DP"6,Q"3$),`DQ,$T)*@DP"3`)04%#0T=#1T=45`DJ"G,P
M8PDP"6,Q"3$),`DQ,$T)*@DP"3`)04%#0T=#1T=45`DJ"G,Q"3`)8S$),0DP
M"35--DDU30DJ"3`),`E!04-#1T=45$%!0T-'1U14"2H*<S(),`EC,0DQ"3`)
M-4TQ4#1),5`U30DJ"3`),`E!04-#1U1404%#1T=45`DJ"G,S"3`)8S$),0DP
M"35-,TDS4#5-"2H),`DP"4%!0T-'1U140T='5%0)*@IS-`DP"6,Q"3$),`DU
M33-0,TDU30DJ"3`),`E!04-#1T%!0T-'1U14"2H*<S4),`EC,0DQ"3`)-$TQ
M1#)0,DDR4#%$-$T)*@DP"3`)04%#0U1!1T=45`DJ"G,V"3`)8S$),0DP"3)-
<,T0V23-$,DT)*@DP"3`)04%'5%1!04-45`DJ"@``
`
end