How to convert from a cigar string to extended cigar string?

Question

[omariqbal2017]

I have a cigar string and the MD tag of the corresponding read record and I want to get the extended cigar string. Is there any java/c/c++ code or library that allows me to do that?

[Pierre Lindenbaum]

what is an "extended cigar string" ? give an example of input / output.

[WouterDeCoster]

AFAIK nucleotide match/mismatch (X,=) instead of a alignment match (M).

[omariqbal2017]

2 examples: - cigar string "100M" MD tag "43C5C43T6" output = "43=C5=C43=T6=".

• cigar string "80M1I19M" MD tag "63T26C8" output = "63=T16=1+9=C9="

Answer 1

[GenoMax]

reformat.sh from BBMap suite.

reformat.sh in=your.bam out=new.bam sam=1.4

Answer 2

[Pierre Lindenbaum]

I wrote samfixcigar : http://lindenb.github.io/jvarkit/SamFixCigar.html

$ cat toy.sam

@SQ     SN:ref  LN:45
@SQ     SN:ref2 LN:40
r001    163     ref     7       30      8M4I4M1D3M      =       37      39      TTAGATAAAGAGGATACTG     *       XX:B:S,12561,2,20,112
r002    0       ref     9       30      1S2I6M1P1I1P1I4M2I      *       0       0       AAAAGATAAGGGATAAA       *
r003    0       ref     9       30      5H6M    *       0       0       AGCTAA  *
r004    0       ref     16      30      6M14N1I5M       *       0       0       ATAGCTCTCAGC    *
r003    16      ref     29      30      6H5M    *       0       0       TAGGC   *
r001    83      ref     37      30      9M      =       7       -39     CAGCGCCAT       *
x1      0       ref2    1       30      20M     *       0       0       aggttttataaaacaaataa    ????????????????????
x2      0       ref2    2       30      21M     *       0       0       ggttttataaaacaaataatt   ?????????????????????
x3      0       ref2    6       30      9M4I13M *       0       0       ttataaaacAAATaattaagtctaca      ??????????????????????????
x4      0       ref2    10      30      25M     *       0       0       CaaaTaattaagtctacagagcaac       ?????????????????????????
x5      0       ref2    12      30      24M     *       0       0       aaTaattaagtctacagagcaact        ????????????????????????
x6      0       ref2    14      30      23M     *       0       0       Taattaagtctacagagcaacta ???????????????????????

$ java -jar dist/samfixcigar.jar \
     -r samtools-0.1.19/examples/toy.fa \
     samtools-0.1.19/examples/toy.sam

output:

@HD     VN:1.4  SO:unsorted
@SQ     SN:ref  LN:45
@SQ     SN:ref2 LN:40
r001    163     ref     7       30      8=4I4=1D3=      =       37      39      TTAGATAAAGAGGATACTG     *       XX:B:S,12561,2,20,112
r002    0       ref     9       30      1S2I6=1P1I1P1I1X1=2X2I  *       0       0       AAAAGATAAGGGATAAA       *
r003    0       ref     9       30      2=1X3=  *       0       0       AGCTAA  *
r004    0       ref     16      30      6=14N1I5=       *       0       0       ATAGCTCTCAGC    *
r003    16      ref     29      30      5=      *       0       0       TAGGC   *
r001    83      ref     37      30      9=      =       7       -39     CAGCGCCAT       *
x1      0       ref2    1       30      16=1X3= *       0       0       AGGTTTTATAAAACAAATAA    ????????????????????
x2      0       ref2    2       30      15=1X3=1X1=     *       0       0       GGTTTTATAAAACAAATAATT   ?????????????????????
x3      0       ref2    6       30      9=4I13= *       0       0       TTATAAAACAAATAATTAAGTCTACA      ??????????????????????????
x4      0       ref2    10      30      1X3=1X20=       *       0       0       CAAATAATTAAGTCTACAGAGCAAC       ?????????????????????????
x5      0       ref2    12      30      2=1X21= *       0       0       AATAATTAAGTCTACAGAGCAACT        ????????????????????????
x6      0       ref2    14      30      1X22=   *       0       0       TAATTAAGTCTACAGAGCAACTA ???????????????????????