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when I use the model of the modify bamAssign, if the -r added, the header of the output SAM/BAM will keep its own chromosomes. but it is just output a little reads and the header of the bam just include the "@sq SN:chr1 LN:31279297" without other information such as "@rg @pg". when I use the samtools view to open the the output bam, it is display [main_samview] truncated file. So, what is the problem?

Hi,

I extracted individual contigs from a bam file using:

BamDeal_Linux modify bamSplit -r -i me14.sorted.again.bam
and
BamDeal_Linux modify bamSplit -i me14.sorted.again.bam

However, when I try to index the extracted contigs with samtools (1.13) I get this error:

samtools index ArME14_ctg_01.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read_block] Failed to read BGZF block data at offset 1146092758 expected 7118 bytes; hread returned 792
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
samtools index: failed to create index for "ArME14_ctg_01.bam": No such file or directory

Trying to index the original bam file me14.sorted.again.bam works just fine.
Any idea what is going on?

I am using BamDeal 0.25

Cheers,
Johannes

I'm having a problem compiling the macOS executable.

"./src/convert/../ALL/../ALL/msort/msort_h.h:828:1: warning: control reaches end of non-void function [-Wreturn-type]"

"./src/statistics/Bmath/pnorm.c:98:11: error: no member named 'isnan' in namespace 'std'; did you mean simply 'isnan'?"

"./src/statistics/BamDeteSV.h:343:5: warning: array index 2 is past the end of the array (which contains 2 elements) [-Warray-bounds]"