[Debian-med-packaging] Bug#1022282: staden-io-lib: FTBFS: ./data/9827_rand3.cram.fai: No such file or directory

[Lucas Nussbaum]

Source: staden-io-lib
Version: 1.14.14+dfsg-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221023 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[3]: Entering directory '/<<PKGBUILDDIR>>/tests'
> PASS: srf2fasta.test
> PASS: srf2fastq.test
> PASS: srf_info.test
> Reading archive ./data/both.srf.
> PASS: srf_filter.test
> NB: The next line is expected to be an error message
> Malformed or missing index hash. Consider running srf_index_hash
> Nbuckets  = 16
> Nused     = 20
> Avg chain = 1.250000
> Chain var.= 0.812500
> %age full = 81.250000
> max len   = 3
> Chain  0   = 3
> Chain  1   = 8
> Chain  2   = 3
> Chain  3   = 2
> PASS: srf_index.test
> Loading ce.fa
> Generating ce#sorted.sam
> Generating ce#unsorted.sam
> === testing ./data/c1#bounds.sam ===
>  ../progs/scramble  ./data/c1#bounds.sam test.out/c1#bounds.bam
>  ../progs/scramble   -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  test.out/c1#bounds.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
>  ../progs/scramble   -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
>  ../progs/scramble  test.out/c1#bounds.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble   -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble   -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble   -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
> 
> === testing ./data/c1#clip.sam ===
>  ../progs/scramble  ./data/c1#clip.sam test.out/c1#clip.bam
>  ../progs/scramble   -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  test.out/c1#clip.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
>  ../progs/scramble   -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
>  ../progs/scramble  test.out/c1#clip.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble   -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble   -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble   -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
> 
> === testing ./data/c1#pad1.sam ===
>  ../progs/scramble  ./data/c1#pad1.sam test.out/c1#pad1.bam
>  ../progs/scramble   -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  test.out/c1#pad1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
>  ../progs/scramble   -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
>  ../progs/scramble  test.out/c1#pad1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble   -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble   -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble   -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
> 
> === testing ./data/c1#pad2.sam ===
>  ../progs/scramble  ./data/c1#pad2.sam test.out/c1#pad2.bam
>  ../progs/scramble   -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  test.out/c1#pad2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
>  ../progs/scramble   -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
>  ../progs/scramble  test.out/c1#pad2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble   -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble   -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble   -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
> 
> === testing ./data/c1#pad3.sam ===
>  ../progs/scramble  ./data/c1#pad3.sam test.out/c1#pad3.bam
>  ../progs/scramble   -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  test.out/c1#pad3.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
>  ../progs/scramble   -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
>  ../progs/scramble  test.out/c1#pad3.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble   -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble   -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble   -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
> 
> === testing ./data/ce#1.sam ===
>  ../progs/scramble  ./data/ce#1.sam test.out/ce#1.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  test.out/ce#1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
>  ../progs/scramble   -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
>  ../progs/scramble  test.out/ce#1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
> 
> === testing ./data/ce#2.sam ===
>  ../progs/scramble  ./data/ce#2.sam test.out/ce#2.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  test.out/ce#2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
>  ../progs/scramble   -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
>  ../progs/scramble  test.out/ce#2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
> 
> === testing ./data/ce#5.sam ===
>  ../progs/scramble  ./data/ce#5.sam test.out/ce#5.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  test.out/ce#5.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
>  ../progs/scramble   -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
>  ../progs/scramble  test.out/ce#5.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
> 
> === testing ./data/ce#5b.sam ===
>  ../progs/scramble  ./data/ce#5b.sam test.out/ce#5b.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  test.out/ce#5b.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
>  ../progs/scramble   -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
>  ../progs/scramble  test.out/ce#5b.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
> 
> === testing ./data/ce#large_seq.sam ===
>  ../progs/scramble  ./data/ce#large_seq.sam test.out/ce#large_seq.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  test.out/ce#large_seq.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
>  ../progs/scramble   -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
>  ../progs/scramble  test.out/ce#large_seq.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
> 
> === testing ./data/ce#sorted.sam ===
>  ../progs/scramble  ./data/ce#sorted.sam test.out/ce#sorted.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  test.out/ce#sorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
>  ../progs/scramble   -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
>  ../progs/scramble  test.out/ce#sorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
> 
> === testing ./data/ce#tag_depadded.sam ===
>  ../progs/scramble  ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  test.out/ce#tag_depadded.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
>  ../progs/scramble   -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
>  ../progs/scramble  test.out/ce#tag_depadded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
> 
> === testing ./data/ce#tag_padded.sam ===
>  ../progs/scramble  ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  test.out/ce#tag_padded.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
>  ../progs/scramble   -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
>  ../progs/scramble  test.out/ce#tag_padded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
> 
> === testing ./data/ce#unmap.sam ===
>  ../progs/scramble  ./data/ce#unmap.sam test.out/ce#unmap.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  test.out/ce#unmap.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
>  ../progs/scramble   -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
>  ../progs/scramble  test.out/ce#unmap.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
> 
> === testing ./data/ce#unmap1.sam ===
>  ../progs/scramble  ./data/ce#unmap1.sam test.out/ce#unmap1.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble  test.out/ce#unmap1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
>  ../progs/scramble   -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
>  ../progs/scramble  test.out/ce#unmap1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble  test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
> 
> === testing ./data/ce#unmap2.sam ===
>  ../progs/scramble  ./data/ce#unmap2.sam test.out/ce#unmap2.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble  test.out/ce#unmap2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
>  ../progs/scramble   -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
>  ../progs/scramble  test.out/ce#unmap2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble   -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble   -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble  test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
> 
> === testing ./data/ce#unsorted.sam ===
>  ../progs/scramble  ./data/ce#unsorted.sam test.out/ce#unsorted.bam
>  ../progs/scramble   -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble  test.out/ce#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
>  ../progs/scramble   -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
>  ../progs/scramble  test.out/ce#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
>  ../progs/scramble   -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble  test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
> 
> === testing ./data/tag_aux#aux.sam ===
>  ../progs/scramble  ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
>  ../progs/scramble   -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble  test.out/tag_aux#aux.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
>  ../progs/scramble   -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
>  ../progs/scramble  test.out/tag_aux#aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble   -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble   -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble   -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble  test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
> 
> === testing ./data/tag_aux#special.sam ===
>  ../progs/scramble  ./data/tag_aux#special.sam test.out/tag_aux#special.bam
>  ../progs/scramble   -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble  test.out/tag_aux#special.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
>  ../progs/scramble   -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
>  ../progs/scramble  test.out/tag_aux#special.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble   -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble   -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble   -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble  test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
> 
> === testing ./data/tag_aux#values1.bam ===
>  ../progs/scramble  ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
>  ../progs/scramble   -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble  ./data/tag_aux#values1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
>  ../progs/scramble   -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
>  ../progs/scramble  test.out/tag_aux#values1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble   -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble   -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble   -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble  test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
> 
> === testing ./data/tag_aux#values2.bam ===
>  ../progs/scramble  ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
>  ../progs/scramble   -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble  ./data/tag_aux#values2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
>  ../progs/scramble   -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
>  ../progs/scramble  test.out/tag_aux#values2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble   -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble   -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble   -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble  test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
> 
> === testing ./data/tag_aux#values4.bam ===
>  ../progs/scramble  ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
>  ../progs/scramble   -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble  ./data/tag_aux#values4.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
>  ../progs/scramble   -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
>  ../progs/scramble  test.out/tag_aux#values4.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble   -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble   -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble   -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble  test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
> 
> === testing ./data/xx#MD.sam ===
>  ../progs/scramble  ./data/xx#MD.sam test.out/xx#MD.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  test.out/xx#MD.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
>  ../progs/scramble   -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
>  ../progs/scramble  test.out/xx#MD.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
> 
> === testing ./data/xx#MD2.sam ===
>  ../progs/scramble  ./data/xx#MD2.sam test.out/xx#MD2.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  test.out/xx#MD2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
>  ../progs/scramble   -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
>  ../progs/scramble  test.out/xx#MD2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
> 
> === testing ./data/xx#blank.sam ===
>  ../progs/scramble  ./data/xx#blank.sam test.out/xx#blank.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  test.out/xx#blank.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
>  ../progs/scramble   -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
>  ../progs/scramble  test.out/xx#blank.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
> 
> === testing ./data/xx#large_aux.sam ===
>  ../progs/scramble  ./data/xx#large_aux.sam test.out/xx#large_aux.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  test.out/xx#large_aux.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
>  ../progs/scramble   -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
>  ../progs/scramble  test.out/xx#large_aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
> 
> === testing ./data/xx#large_aux2.sam ===
>  ../progs/scramble  ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  test.out/xx#large_aux2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
>  ../progs/scramble   -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
>  ../progs/scramble  test.out/xx#large_aux2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
> 
> === testing ./data/xx#minimal.sam ===
>  ../progs/scramble  ./data/xx#minimal.sam test.out/xx#minimal.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  test.out/xx#minimal.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
>  ../progs/scramble   -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
>  ../progs/scramble  test.out/xx#minimal.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
> 
> === testing ./data/xx#pair.sam ===
>  ../progs/scramble  ./data/xx#pair.sam test.out/xx#pair.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  test.out/xx#pair.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
>  ../progs/scramble   -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
>  ../progs/scramble  test.out/xx#pair.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
> 
> === testing ./data/xx#repeated.sam ===
>  ../progs/scramble  ./data/xx#repeated.sam test.out/xx#repeated.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  test.out/xx#repeated.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
>  ../progs/scramble   -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
>  ../progs/scramble  test.out/xx#repeated.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
> 
> === testing ./data/xx#rg.sam ===
>  ../progs/scramble  ./data/xx#rg.sam test.out/xx#rg.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  test.out/xx#rg.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
>  ../progs/scramble   -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
>  ../progs/scramble  test.out/xx#rg.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
> 
> === testing ./data/xx#triplet.sam ===
>  ../progs/scramble  ./data/xx#triplet.sam test.out/xx#triplet.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  test.out/xx#triplet.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
>  ../progs/scramble   -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
>  ../progs/scramble  test.out/xx#triplet.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble   -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble   -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
> 
> === testing ./data/xx#unsorted.sam ===
>  ../progs/scramble  ./data/xx#unsorted.sam test.out/xx#unsorted.bam
>  ../progs/scramble   -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble  test.out/xx#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
>  ../progs/scramble   -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
>  ../progs/scramble  test.out/xx#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
>  ../progs/scramble   -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble  test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
> 
> PASS: scram.test
> === testing ./data/c1#bounds.sam ===
>  ../progs/scramble  ./data/c1#bounds.sam test.out/c1#bounds.bam
>  ../progs/scramble  -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  test.out/c1#bounds.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
>  ../progs/scramble  test.out/c1#bounds.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble  test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
> 
> === testing ./data/c1#clip.sam ===
>  ../progs/scramble  ./data/c1#clip.sam test.out/c1#clip.bam
>  ../progs/scramble  -V3.0 -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  test.out/c1#clip.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
>  ../progs/scramble  test.out/c1#clip.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble  test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
> 
> === testing ./data/c1#pad1.sam ===
>  ../progs/scramble  ./data/c1#pad1.sam test.out/c1#pad1.bam
>  ../progs/scramble  -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  test.out/c1#pad1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
>  ../progs/scramble  test.out/c1#pad1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble  test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
> 
> === testing ./data/c1#pad2.sam ===
>  ../progs/scramble  ./data/c1#pad2.sam test.out/c1#pad2.bam
>  ../progs/scramble  -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  test.out/c1#pad2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
>  ../progs/scramble  test.out/c1#pad2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble  test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
> 
> === testing ./data/c1#pad3.sam ===
>  ../progs/scramble  ./data/c1#pad3.sam test.out/c1#pad3.bam
>  ../progs/scramble  -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  test.out/c1#pad3.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
>  ../progs/scramble  test.out/c1#pad3.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble  test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
> 
> === testing ./data/ce#1.sam ===
>  ../progs/scramble  ./data/ce#1.sam test.out/ce#1.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  test.out/ce#1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
>  ../progs/scramble  test.out/ce#1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble  test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
> 
> === testing ./data/ce#2.sam ===
>  ../progs/scramble  ./data/ce#2.sam test.out/ce#2.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  test.out/ce#2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
>  ../progs/scramble  test.out/ce#2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble  test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
> 
> === testing ./data/ce#5.sam ===
>  ../progs/scramble  ./data/ce#5.sam test.out/ce#5.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  test.out/ce#5.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
>  ../progs/scramble  test.out/ce#5.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble  test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
> 
> === testing ./data/ce#5b.sam ===
>  ../progs/scramble  ./data/ce#5b.sam test.out/ce#5b.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  test.out/ce#5b.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
>  ../progs/scramble  test.out/ce#5b.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble  test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
> 
> === testing ./data/ce#large_seq.sam ===
>  ../progs/scramble  ./data/ce#large_seq.sam test.out/ce#large_seq.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  test.out/ce#large_seq.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
>  ../progs/scramble  test.out/ce#large_seq.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble  test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
> 
> === testing ./data/ce#sorted.sam ===
>  ../progs/scramble  ./data/ce#sorted.sam test.out/ce#sorted.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  test.out/ce#sorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
>  ../progs/scramble  test.out/ce#sorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble  test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
> 
> === testing ./data/ce#tag_depadded.sam ===
>  ../progs/scramble  ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  test.out/ce#tag_depadded.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
>  ../progs/scramble  test.out/ce#tag_depadded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble  test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
> 
> === testing ./data/ce#tag_padded.sam ===
>  ../progs/scramble  ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  test.out/ce#tag_padded.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
>  ../progs/scramble  test.out/ce#tag_padded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble  test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
> 
> === testing ./data/ce#unmap.sam ===
>  ../progs/scramble  ./data/ce#unmap.sam test.out/ce#unmap.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  test.out/ce#unmap.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
>  ../progs/scramble  test.out/ce#unmap.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble  test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
> 
> === testing ./data/ce#unmap1.sam ===
>  ../progs/scramble  ./data/ce#unmap1.sam test.out/ce#unmap1.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble  test.out/ce#unmap1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
>  ../progs/scramble  test.out/ce#unmap1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble  test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
> 
> === testing ./data/ce#unmap2.sam ===
>  ../progs/scramble  ./data/ce#unmap2.sam test.out/ce#unmap2.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble  test.out/ce#unmap2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
>  ../progs/scramble  test.out/ce#unmap2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble  test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
> 
> === testing ./data/ce#unsorted.sam ===
>  ../progs/scramble  ./data/ce#unsorted.sam test.out/ce#unsorted.bam
>  ../progs/scramble  -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble  test.out/ce#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
>  ../progs/scramble  test.out/ce#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble  test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
> 
> === testing ./data/tag_aux#aux.sam ===
>  ../progs/scramble  ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
>  ../progs/scramble  -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble  test.out/tag_aux#aux.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
>  ../progs/scramble  test.out/tag_aux#aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble  test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
> 
> === testing ./data/tag_aux#special.sam ===
>  ../progs/scramble  ./data/tag_aux#special.sam test.out/tag_aux#special.bam
>  ../progs/scramble  -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble  test.out/tag_aux#special.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
>  ../progs/scramble  test.out/tag_aux#special.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble  test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
> 
> === testing ./data/tag_aux#values1.bam ===
>  ../progs/scramble  ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
>  ../progs/scramble  -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble  ./data/tag_aux#values1.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
>  ../progs/scramble  test.out/tag_aux#values1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble  test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
> 
> === testing ./data/tag_aux#values2.bam ===
>  ../progs/scramble  ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
>  ../progs/scramble  -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble  ./data/tag_aux#values2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
>  ../progs/scramble  test.out/tag_aux#values2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble  test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
> 
> === testing ./data/tag_aux#values4.bam ===
>  ../progs/scramble  ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
>  ../progs/scramble  -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble  ./data/tag_aux#values4.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
>  ../progs/scramble  test.out/tag_aux#values4.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble  -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble  test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
> 
> === testing ./data/xx#MD.sam ===
>  ../progs/scramble  ./data/xx#MD.sam test.out/xx#MD.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  test.out/xx#MD.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
>  ../progs/scramble  test.out/xx#MD.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble  test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
> 
> === testing ./data/xx#MD2.sam ===
>  ../progs/scramble  ./data/xx#MD2.sam test.out/xx#MD2.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  test.out/xx#MD2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
>  ../progs/scramble  test.out/xx#MD2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble  test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
> 
> === testing ./data/xx#blank.sam ===
>  ../progs/scramble  ./data/xx#blank.sam test.out/xx#blank.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  test.out/xx#blank.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
>  ../progs/scramble  test.out/xx#blank.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble  test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
> 
> === testing ./data/xx#large_aux.sam ===
>  ../progs/scramble  ./data/xx#large_aux.sam test.out/xx#large_aux.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  test.out/xx#large_aux.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
>  ../progs/scramble  test.out/xx#large_aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble  test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
> 
> === testing ./data/xx#large_aux2.sam ===
>  ../progs/scramble  ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  test.out/xx#large_aux2.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
>  ../progs/scramble  test.out/xx#large_aux2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble  test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
> 
> === testing ./data/xx#minimal.sam ===
>  ../progs/scramble  ./data/xx#minimal.sam test.out/xx#minimal.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  test.out/xx#minimal.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
>  ../progs/scramble  test.out/xx#minimal.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble  test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
> 
> === testing ./data/xx#pair.sam ===
>  ../progs/scramble  ./data/xx#pair.sam test.out/xx#pair.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  test.out/xx#pair.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
>  ../progs/scramble  test.out/xx#pair.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble  test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
> 
> === testing ./data/xx#repeated.sam ===
>  ../progs/scramble  ./data/xx#repeated.sam test.out/xx#repeated.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  test.out/xx#repeated.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
>  ../progs/scramble  test.out/xx#repeated.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble  test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
> 
> === testing ./data/xx#rg.sam ===
>  ../progs/scramble  ./data/xx#rg.sam test.out/xx#rg.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  test.out/xx#rg.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
>  ../progs/scramble  test.out/xx#rg.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble  test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
> 
> === testing ./data/xx#triplet.sam ===
>  ../progs/scramble  ./data/xx#triplet.sam test.out/xx#triplet.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  test.out/xx#triplet.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
>  ../progs/scramble  test.out/xx#triplet.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble  -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble  -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble  test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
> 
> === testing ./data/xx#unsorted.sam ===
>  ../progs/scramble  ./data/xx#unsorted.sam test.out/xx#unsorted.bam
>  ../progs/scramble  -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble  test.out/xx#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble  -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
>  ../progs/scramble  -V3.0 -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
>  ../progs/scramble  test.out/xx#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
>  ../progs/scramble  -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble  test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
> 
> === testing ./data/c1#bounds.sam ===
>  ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
>  ../progs/scramble -t4  -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
>  ../progs/scramble -t4  -O bam test.out/c1#bounds.full.cram > test.out/c1#bounds.full.bam
>  ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam test.out/c1#bounds.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
>  ../progs/scramble -t4 test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#bounds.sam test.out/c1#bounds.full.bam.sam
> 
> === testing ./data/c1#clip.sam ===
>  ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam
>  ../progs/scramble -t4  -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
>  ../progs/scramble -t4  -O bam test.out/c1#clip.full.cram > test.out/c1#clip.full.bam
>  ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble -t4 -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam test.out/c1#clip.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/c1.fa test.out/c1#clip.bam test.out/c1#clip.full.cram
>  ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam
> 
> === testing ./data/c1#pad1.sam ===
>  ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam
>  ../progs/scramble -t4  -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
>  ../progs/scramble -t4  -O bam test.out/c1#pad1.full.cram > test.out/c1#pad1.full.bam
>  ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam test.out/c1#pad1.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/c1.fa test.out/c1#pad1.bam test.out/c1#pad1.full.cram
>  ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam
> 
> === testing ./data/c1#pad2.sam ===
>  ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam
>  ../progs/scramble -t4  -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
>  ../progs/scramble -t4  -O bam test.out/c1#pad2.full.cram > test.out/c1#pad2.full.bam
>  ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam test.out/c1#pad2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/c1.fa test.out/c1#pad2.bam test.out/c1#pad2.full.cram
>  ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam
> 
> === testing ./data/c1#pad3.sam ===
>  ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam
>  ../progs/scramble -t4  -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
>  ../progs/scramble -t4  -O bam test.out/c1#pad3.full.cram > test.out/c1#pad3.full.bam
>  ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam test.out/c1#pad3.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/c1.fa test.out/c1#pad3.bam test.out/c1#pad3.full.cram
>  ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam
> ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam
> 
> === testing ./data/ce#1.sam ===
>  ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam
>  ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam test.out/ce#1.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram
>  ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam
> 
> === testing ./data/ce#2.sam ===
>  ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam
>  ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam test.out/ce#2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram
>  ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam
> 
> === testing ./data/ce#5.sam ===
>  ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam
>  ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam test.out/ce#5.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram
>  ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam
> 
> === testing ./data/ce#5b.sam ===
>  ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam
>  ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam test.out/ce#5b.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#5b.bam test.out/ce#5b.full.cram
>  ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam
> 
> === testing ./data/ce#large_seq.sam ===
>  ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.bam
>  ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam test.out/ce#large_seq.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#large_seq.bam test.out/ce#large_seq.full.cram
>  ../progs/scramble -t4 test.out/ce#large_seq.full.cram > test.out/ce#large_seq.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam test.out/ce#large_seq.full.bam.sam
> 
> === testing ./data/ce#sorted.sam ===
>  ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#sorted.full.cram > test.out/ce#sorted.full.bam
>  ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam test.out/ce#sorted.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#sorted.bam test.out/ce#sorted.full.cram
>  ../progs/scramble -t4 test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#sorted.sam test.out/ce#sorted.full.bam.sam
> 
> === testing ./data/ce#tag_depadded.sam ===
>  ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.bam
>  ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam test.out/ce#tag_depadded.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#tag_depadded.bam test.out/ce#tag_depadded.full.cram
>  ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > test.out/ce#tag_depadded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.full.bam.sam
> 
> === testing ./data/ce#tag_padded.sam ===
>  ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.bam
>  ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam test.out/ce#tag_padded.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#tag_padded.bam test.out/ce#tag_padded.full.cram
>  ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > test.out/ce#tag_padded.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam test.out/ce#tag_padded.full.bam.sam
> 
> === testing ./data/ce#unmap.sam ===
>  ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#unmap.full.cram > test.out/ce#unmap.full.bam
>  ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam test.out/ce#unmap.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#unmap.bam test.out/ce#unmap.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap.sam test.out/ce#unmap.full.bam.sam
> 
> === testing ./data/ce#unmap1.sam ===
>  ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.bam
>  ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam test.out/ce#unmap1.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#unmap1.bam test.out/ce#unmap1.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam test.out/ce#unmap1.full.bam.sam
> 
> === testing ./data/ce#unmap2.sam ===
>  ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.bam
>  ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam test.out/ce#unmap2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#unmap2.bam test.out/ce#unmap2.full.cram
>  ../progs/scramble -t4 test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam test.out/ce#unmap2.full.bam.sam
> 
> === testing ./data/ce#unsorted.sam ===
>  ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam
>  ../progs/scramble -t4  -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
>  ../progs/scramble -t4  -O bam test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.bam
>  ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam test.out/ce#unsorted.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/ce.fa test.out/ce#unsorted.bam test.out/ce#unsorted.full.cram
>  ../progs/scramble -t4 test.out/ce#unsorted.full.cram > test.out/ce#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam test.out/ce#unsorted.full.bam.sam
> 
> === testing ./data/tag_aux#aux.sam ===
>  ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam
>  ../progs/scramble -t4  -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
>  ../progs/scramble -t4  -O bam test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.bam
>  ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam test.out/tag_aux#aux.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam test.out/tag_aux#aux.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > test.out/tag_aux#aux.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam test.out/tag_aux#aux.full.bam.sam
> 
> === testing ./data/tag_aux#special.sam ===
>  ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam
>  ../progs/scramble -t4  -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
>  ../progs/scramble -t4  -O bam test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.bam
>  ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam test.out/tag_aux#special.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#special.full.cram > test.out/tag_aux#special.full.sam
> ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam test.out/tag_aux#special.full.bam.sam
> 
> === testing ./data/tag_aux#values1.bam ===
>  ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam
>  ../progs/scramble -t4  -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
>  ../progs/scramble -t4  -O bam test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.bam
>  ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam test.out/tag_aux#values1.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam test.out/tag_aux#values1.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > test.out/tag_aux#values1.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam test.out/tag_aux#values1.full.bam.sam
> 
> === testing ./data/tag_aux#values2.bam ===
>  ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam
>  ../progs/scramble -t4  -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
>  ../progs/scramble -t4  -O bam test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.bam
>  ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam test.out/tag_aux#values2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam test.out/tag_aux#values2.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > test.out/tag_aux#values2.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam test.out/tag_aux#values2.full.bam.sam
> 
> === testing ./data/tag_aux#values4.bam ===
>  ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam
>  ../progs/scramble -t4  -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
>  ../progs/scramble -t4  -O bam test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.bam
>  ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded reference with non-coordinate sorted data is not supported.
> Using -x for no-ref instead.
>  ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
> Embedded consensus with non-coordinate sorted data is not supported.
>  ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam test.out/tag_aux#values4.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam test.out/tag_aux#values4.full.cram
>  ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > test.out/tag_aux#values4.full.sam
> ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam test.out/tag_aux#values4.full.bam.sam
> 
> === testing ./data/xx#MD.sam ===
>  ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam
>  ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam test.out/xx#MD.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#MD.bam test.out/xx#MD.full.cram
>  ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam
> 
> === testing ./data/xx#MD2.sam ===
>  ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#MD2.full.cram > test.out/xx#MD2.full.bam
>  ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam test.out/xx#MD2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#MD2.bam test.out/xx#MD2.full.cram
>  ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam
> 
> === testing ./data/xx#blank.sam ===
>  ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#blank.full.cram > test.out/xx#blank.full.bam
>  ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble -t4 -m test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam test.out/xx#blank.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#blank.bam test.out/xx#blank.full.cram
>  ../progs/scramble -t4 test.out/xx#blank.full.cram > test.out/xx#blank.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#blank.sam test.out/xx#blank.full.bam.sam
> 
> === testing ./data/xx#large_aux.sam ===
>  ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.bam
>  ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam test.out/xx#large_aux.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#large_aux.bam test.out/xx#large_aux.full.cram
>  ../progs/scramble -t4 test.out/xx#large_aux.full.cram > test.out/xx#large_aux.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam test.out/xx#large_aux.full.bam.sam
> 
> === testing ./data/xx#large_aux2.sam ===
>  ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.bam
>  ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam test.out/xx#large_aux2.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#large_aux2.bam test.out/xx#large_aux2.full.cram
>  ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > test.out/xx#large_aux2.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam test.out/xx#large_aux2.full.bam.sam
> 
> === testing ./data/xx#minimal.sam ===
>  ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#minimal.full.cram > test.out/xx#minimal.full.bam
>  ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam test.out/xx#minimal.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#minimal.bam test.out/xx#minimal.full.cram
>  ../progs/scramble -t4 test.out/xx#minimal.full.cram > test.out/xx#minimal.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#minimal.sam test.out/xx#minimal.full.bam.sam
> 
> === testing ./data/xx#pair.sam ===
>  ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#pair.full.cram > test.out/xx#pair.full.bam
>  ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble -t4 -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam test.out/xx#pair.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#pair.bam test.out/xx#pair.full.cram
>  ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam
> 
> === testing ./data/xx#repeated.sam ===
>  ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#repeated.full.cram > test.out/xx#repeated.full.bam
>  ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam test.out/xx#repeated.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#repeated.bam test.out/xx#repeated.full.cram
>  ../progs/scramble -t4 test.out/xx#repeated.full.cram > test.out/xx#repeated.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#repeated.sam test.out/xx#repeated.full.bam.sam
> 
> === testing ./data/xx#rg.sam ===
>  ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam
>  ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam test.out/xx#rg.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#rg.bam test.out/xx#rg.full.cram
>  ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam
> 
> === testing ./data/xx#triplet.sam ===
>  ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#triplet.full.cram > test.out/xx#triplet.full.bam
>  ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble -t4  -e -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble -t4  -E -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam test.out/xx#triplet.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#triplet.bam test.out/xx#triplet.full.cram
>  ../progs/scramble -t4 test.out/xx#triplet.full.cram > test.out/xx#triplet.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#triplet.sam test.out/xx#triplet.full.bam.sam
> 
> === testing ./data/xx#unsorted.sam ===
>  ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam
>  ../progs/scramble -t4  -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam
>  ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
>  ../progs/scramble -t4  -O bam test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.bam
>  ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam
> ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam test.out/xx#unsorted.full.bam.sam
>  ../progs/scramble -t4  -x -r ./data/xx.fa test.out/xx#unsorted.bam test.out/xx#unsorted.full.cram
>  ../progs/scramble -t4 test.out/xx#unsorted.full.cram > test.out/xx#unsorted.full.sam
> ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam test.out/xx#unsorted.full.bam.sam
> 
> PASS: scram_mt30.test
> === testing ./data/c1#bounds.sam ===
>  ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
>  ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
> 
> WARNING: this version of CRAM is not a recognised GA4GH standard.
> Note this CRAM version is a technology demonstration only.
> Future versions of Scramble may not be able to read these files.
> 
> Segmentation fault
> FAIL: scram_mt31.test
> === testing ./data/c1#bounds.sam ===
>  ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam
>  ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam test.out/c1#bounds.full.cram
> 
> WARNING: this version of CRAM is not a recognised GA4GH standard.
> Note this CRAM version is a technology demonstration only.
> Future versions of Scramble may not be able to read these files.
> 
> Segmentation fault
> FAIL: scram_mt40.test
> PASS: cram_io.test
> === testing ./data/ce#5b_java.cram ===
>  ../progs/scramble  -t4 -r ./data/ce.fa ./data/ce#5b_java.cram test.out/ce#5b_java.scramble.sam
> ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam
> === testing ./data/tag_aux#aux_java.cram ===
>  ../progs/scramble  -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram test.out/tag_aux#aux_java.scramble.sam
> ./compare_sam.pl ./data/tag_aux#aux_java.sam test.out/tag_aux#aux_java.scramble.sam
> === testing ./data/xx#large_aux_java.cram ===
>  ../progs/scramble  -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram test.out/xx#large_aux_java.scramble.sam
> ./compare_sam.pl ./data/xx#large_aux_java.sam test.out/xx#large_aux_java.scramble.sam
> === testing ./data/9827_rand3.cram ===
>  ../progs/scramble  -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram test.out/9827_rand3.scramble.sam
> ./data/9827_rand3.cram.fai: No such file or directory
> ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam
> PASS: java.test
> ====================
> 2 of 11 tests failed
> ====================
> make[3]: *** [Makefile:529: check-TESTS] Error 1
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests'
> make[2]: *** [Makefile:657: check-am] Error 2
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests'
> make[1]: *** [Makefile:759: check-recursive] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2


The full build log is available from:
http://qa-logs.debian.net/2022/10/23/staden-io-lib_1.14.14+dfsg-1_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221023;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221023&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.