Breakdancer bam2cfg.pl emtpy output with multiple readgroups

[mak]

Hallo everyone,

This has been bugging me for a few days now, I get empty output from bam2cfg.pl from my merged bam file. I've seen many threads but non of them helped me fix my problem. I have a merged bam file (merged with picard-tools) consisting out of 4 paired end samples of the same individual. The following command has no output:

$ perl bam2cfg.pl testdata.newbam.bam > break.cfg

My bam files looks like this:

@HD     GO:none VN:1.4  SO:coordinate
@SQ     SN:chrM LN:16569
@SQ     SN:chr1 LN:249250621
@SQ     SN:chr2 LN:243199373
@SQ     SN:chr3 LN:198022430
@SQ     SN:chr4 LN:191154276
...
@SQ     SN:chrUn_gl000248       LN:39786
@SQ     SN:chrUn_gl000249       LN:38502
@RG     ID:testdata1    DS:tumor        LB:lib  PG:picard-tools PI:455  PL:illumina     PU:bar  SM:testdata
@RG     ID:testdata2    DS:tumor        LB:lib  PG:picard-tools PI:455  PL:illumina     PU:bar  SM:testdata
@RG     ID:testdata3    DS:tumor        LB:lib  PG:picard-tools PI:455  PL:illumina     PU:bar  SM:testdata
@RG     ID:testdata4    DS:tumor        LB:lib  PG:picard-tools PI:455  PL:illumina     PU:bar  SM:testdata
@PG     ID:bwa  PN:bwa  VN:0.5.9-r16
FCC15WDACXX:1:1101:17486:12062  145     chrM    19      37      90M     chr10   44192200        0       CTATTAACCCCTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGA      CDDA85&52(B?><5BCCDBBDDCBCCCDDCBDCDDCCDBDCDCB=DHJJJJIGIJHGFGGHIGIGGGJJIIHEGIIHGHHHFFFFFCCC   RG:Z:testdata1  XT:A:U  NM:i:2  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:9A44A35
FCD1CR7ACXX:5:1101:18187:12124  113     chrM    22      37      90M     chr2    198540778       0       TTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGAGAGCATTGCGAGACGCTGGAGCCGGAGCA      C@<3?:+?8B?BBCCC@@=DDA>D@DC>BCCDDCCDB=88=9A6DHJJIIGIHGG@GHDFD9GGIGIGFCIGIGJJJHHHHHFFFFFCCC   RG:Z:testdata2  XT:A:U  NM:i:2  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:2  XO:i:0  XG:i:0  MD:Z:51A9T28
FCD1CFTACXX:5:1101:7853:10375   65      chrM    30      37      90M     chr18   33913273        0       TCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGT      @B@DDDDDF<DFHIGAFEFEHIIG>B?EGE9D@FGIJIGIIB@B8<>CCB8@8-7<CDDCCA;-88885@B@AA?B@59<<<ABD83AC:   RG:Z:testdata3  XT:A:U  NM:i:1  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:43A46
FCD1CR7ACXX:5:1101:14274:9671   113     chrM    64      37      90M     chr13   34187260        0       CTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCTCA      <<DDDBBBCCA<90BBBDDCDDCBDCBCEFDBGHFIIIGGHIIHFHD;JIEJJJIGGIJJJJGIIJJJIJJJJJJIJHHHGHFFFFFCCC   RG:Z:testdata4  XT:A:U  NM:i:3  SM:i:37 AM:i:37 X0:i:1  X1:i:0  XM:i:3  XO:i:0  XG:i:0  MD:Z:9A77C0T1

Can anyone tell me how to fix it so bam2cfg.pl will work?