What is this result from samtools idxstats?
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8.1 years ago

When running samtools idxstats on an indexed BAM file foo.bam in order to build a list of chromosomes, I get a result that includes a line I'm not sure how to interpret:

$ samtools idxstats foo.bam | cut -f1
chr1
chr10
chr11
...
chrY
*

What is the asterisk supposed to refer to, when I iterate through this list and extract data from that chromosome?

samtools bam bai index • 4.5k views
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Thanks :-) Lige hvad jeg skulle bruge.

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A Møøse once bit my sister...
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8.1 years ago

in the code of bam_index.c

printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);

where n_no_coor = "unmapped reads without coordinate"

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Thanks for the code citation!

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