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dcjones / quip

Compressing next-generation sequencing data with extreme prejudice.
http://www.cs.washington.edu/homes/dcjones/quip/
BSD 3-Clause "New" or "Revised" License
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To SAM/BAM format, Segmentation fault !!! #21

Closed brunoli closed 11 years ago

brunoli commented 11 years ago

1.To SAM format, Can't uncompression ! quip -a xxx.sam -i s # ==> xxx.sam.qp quip -d xxx.sam.qp # ==> Segmentation fault Try: quip -t xxx.sam.sqp # ==>Segmentation fault

  1. To BAM file, Serious data loss! quip -a yyy.bam -i b # ==>yyy.bam.qp 517MB, quip -d yyy.bam.qp # ==> yyy.bam 94MB Try: quip -t # ==> Segmentation fault, samtools view yyy.bam > yyy.sam

    ==>[bam_header_read] EOF marker is absent. The input is probably truncated.

        [main_samview] truncated file.
dcjones commented 11 years ago

Could you tell me what version of quip you are using (by running quip --version)?

brunoli commented 11 years ago

version 1.1.7

dcjones commented 11 years ago

Ok, if you post some example reads I'll see if I can reproduce the bug.

brunoli commented 11 years ago

Prof. Daniel Jones, Your email has been received. I had eight reads(SAM,BAM) compression test, but each apper similar problems(by running quip -a).

One of the reads:

The SAM file: samtools view -h Y725cap.sorted.bam -o Y725cap.sorted.sam The BAM file: Y725cap.sorted.bam Link:https://www.dropbox.com/s/irlaw8pbymmlmmx/Y725cap.sorted.bam

dcjones commented 11 years ago

Thank you for helping me fix this.

I've released a new version that should take care of the problem: http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.8.tar.gz