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sam header is not recognized by awk?

Why doesn't awk recognize the sam header? I match on ^@ and it will print to stdout but not to a file. It prints to stdout but never finishes.

awk '/^@/ {print}' filename

I can't make any sense of this.

Thanks!

sequencing samtools next-gen awk
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updated by Ram Ram • written by mosquitoes • mosquitoes 
awk '/^@/{print}!/^@/{exit}'
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updated by Ram Ram • written by lh3 lh3

2 answers

It prints to stdout but never finishes.

It's got perhaps several dozen headers to read through and print out, followed by perhaps several hundred million alignment records to read though. I'm sure it will finish if you wait long enough!

Perhaps you should consider samtools view -H or similar.

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updated by Ram Ram • written by John Marshall John Marshall

For file 1.t:

@HD VN:1.5 SO:coordinate
@SQ SN:ref LN:45
r001 99 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTG *

awk '/^@/ {print}' 1.t > 2.t

And 2.t will get the output. It works in mawk and gawk.

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updated by Ram Ram • written by Zhilong Jia Zhilong Jia

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