search

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
78 stars 10 forks source link

Fails on a given SAM read #10

Closed westerman closed 12 years ago

westerman commented 12 years ago

The following single-entry sam file fails (i.e., quip just stalls and chews up CPU time). You may need to reformat this for testing purposes. Perhaps obviously this read was surrounded by others. Once I took out this read then quip worked. This read comes via Tophat.

@HD VN:1.0 SO:coordinate @SQ SN:1 LN:30427671 @SQ SN:2 LN:19698289 @SQ SN:3 LN:23459830 @SQ SN:4 LN:18585056 @SQ SN:5 LN:26975502 HWI-ST1234:40:C0WCUACXX:8:1315:2272:91108 0 1 7060 3 10M87N43M1I33M151N14M * 0 0 TCAGTCATCACTTTAAGAGCCATGGAGTTTGATGTTAAGAGAAGTATATCGACAAAAAAAAATCACTGACATTGGGAATTCCCATACCAACATCGC AAGCA CCCFFFFFHHGHHJJJJJJJJJJJJIJHIJJJIJJIJJJIJJJJDHIJJJJIJJJJJJJJGFEDEEEEDDDDDDCBDDDDDDDCCDDDDDDDDDDDDDDDB AS:i:-4 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:100 YT:Z:UU XS:A:- NH:i:2 CC:Z:= CP:i:7060 HI:i:0

dcjones commented 12 years ago

Thanks for finding this. It's fixed in the repository now, and I will put up a new tarball soon.