Menu
▾
▴
Re: [Samtools-help] mpileup segfaults
|
From: Heng Li <lh...@sa...> - 2011-01-27 19:53:04
|
Fixed at the SVN trunk. Thank you, Heng On Jan 25, 2011, at 6:47 PM, Aaron Goodman wrote: > Just wanted to follow up on the Segfault issue. Have you had a chance to look at this? Can I help in any way? > > Regards, > Aaron > > On Thu, Jan 20, 2011 at 4:35 PM, Aaron Goodman <aa...@ge...> wrote: > Certainly. Here is the bam file of the example below. > > Regards, > Aaron > > > On Thu, Jan 20, 2011 at 4:04 PM, Heng Li <lh...@sa...> wrote: > Could you send me a BAM that causes the segfault? > > Many thanks, > > Heng > > > On Jan 20, 2011, at 3:55 PM, Aaron Goodman wrote: > > > Hi All, > > I'm getting a segmentation fault when I run mpileup. I've been able to find the minimal conditions to reproduce the error. The following two reads will cause the problem (using the hg19 reference), and only on the range chr1:660070-660070. It seems like the problem is caused by having a region that is marked as 'N' in one read and 'D' in another. > > > > Regards, > > Aaron > > > > @SQ SN:chr1 LN:249250621 > > @SQ SN:chr2 LN:243199373 > > @SQ SN:chr3 LN:198022430 > > @SQ SN:chr4 LN:191154276 > > @SQ SN:chr5 LN:180915260 > > @SQ SN:chr6 LN:171115067 > > @SQ SN:chr7 LN:159138663 > > @SQ SN:chr8 LN:146364022 > > @SQ SN:chr9 LN:141213431 > > @SQ SN:chr10 LN:135534747 > > @SQ SN:chr11 LN:135006516 > > @SQ SN:chr12 LN:133851895 > > @SQ SN:chr13 LN:115169878 > > @SQ SN:chr14 LN:107349540 > > @SQ SN:chr15 LN:102531392 > > @SQ SN:chr16 LN:90354753 > > @SQ SN:chr17 LN:81195210 > > @SQ SN:chr18 LN:78077248 > > @SQ SN:chr19 LN:59128983 > > @SQ SN:chr20 LN:63025520 > > @SQ SN:chr21 LN:48129895 > > @SQ SN:chr22 LN:51304566 > > @SQ SN:chrX LN:155270560 > > @SQ SN:chrY LN:59373566 > > @SQ SN:chrM LN:16571 > > @SQ SN:chr1_gl000191_random LN:106433 > > @SQ SN:chr1_gl000192_random LN:547496 > > @SQ SN:chr4_ctg9_hap1 LN:590426 > > @SQ SN:chr4_gl000193_random LN:189789 > > @SQ SN:chr4_gl000194_random LN:191469 > > @SQ SN:chr6_apd_hap1 LN:4622290 > > @SQ SN:chr6_cox_hap2 LN:4795371 > > @SQ SN:chr6_dbb_hap3 LN:4610396 > > @SQ SN:chr6_mann_hap4 LN:4683263 > > @SQ SN:chr6_mcf_hap5 LN:4833398 > > @SQ SN:chr6_qbl_hap6 LN:4611984 > > @SQ SN:chr6_ssto_hap7 LN:4928567 > > @SQ SN:chr7_gl000195_random LN:182896 > > @SQ SN:chr8_gl000196_random LN:38914 > > @SQ SN:chr8_gl000197_random LN:37175 > > @SQ SN:chr9_gl000198_random LN:90085 > > @SQ SN:chr9_gl000199_random LN:169874 > > @SQ SN:chr9_gl000200_random LN:187035 > > @SQ SN:chr9_gl000201_random LN:36148 > > @SQ SN:chr11_gl000202_random LN:40103 > > @SQ SN:chr17_ctg5_hap1 LN:1680828 > > @SQ SN:chr17_gl000203_random LN:37498 > > @SQ SN:chr17_gl000204_random LN:81310 > > @SQ SN:chr17_gl000205_random LN:174588 > > @SQ SN:chr17_gl000206_random LN:41001 > > @SQ SN:chr18_gl000207_random LN:4262 > > @SQ SN:chr19_gl000208_random LN:92689 > > @SQ SN:chr19_gl000209_random LN:159169 > > @SQ SN:chr21_gl000210_random LN:27682 > > @SQ SN:chrUn_gl000211 LN:166566 > > @SQ SN:chrUn_gl000212 LN:186858 > > @SQ SN:chrUn_gl000213 LN:164239 > > @SQ SN:chrUn_gl000214 LN:137718 > > @SQ SN:chrUn_gl000215 LN:172545 > > @SQ SN:chrUn_gl000216 LN:172294 > > @SQ SN:chrUn_gl000217 LN:172149 > > @SQ SN:chrUn_gl000218 LN:161147 > > @SQ SN:chrUn_gl000219 LN:179198 > > @SQ SN:chrUn_gl000220 LN:161802 > > @SQ SN:chrUn_gl000221 LN:155397 > > @SQ SN:chrUn_gl000222 LN:186861 > > @SQ SN:chrUn_gl000223 LN:180455 > > @SQ SN:chrUn_gl000224 LN:179693 > > @SQ SN:chrUn_gl000225 LN:211173 > > @SQ SN:chrUn_gl000226 LN:15008 > > @SQ SN:chrUn_gl000227 LN:128374 > > @SQ SN:chrUn_gl000228 LN:129120 > > @SQ SN:chrUn_gl000229 LN:19913 > > @SQ SN:chrUn_gl000230 LN:43691 > > @SQ SN:chrUn_gl000231 LN:27386 > > @SQ SN:chrUn_gl000232 LN:40652 > > @SQ SN:chrUn_gl000233 LN:45941 > > @SQ SN:chrUn_gl000234 LN:40531 > > @SQ SN:chrUn_gl000235 LN:34474 > > @SQ SN:chrUn_gl000236 LN:41934 > > @SQ SN:chrUn_gl000237 LN:45867 > > @SQ SN:chrUn_gl000238 LN:39939 > > @SQ SN:chrUn_gl000239 LN:33824 > > @SQ SN:chrUn_gl000240 LN:41933 > > @SQ SN:chrUn_gl000241 LN:42152 > > @SQ SN:chrUn_gl000242 LN:43523 > > @SQ SN:chrUn_gl000243 LN:43341 > > @SQ SN:chrUn_gl000244 LN:39929 > > @SQ SN:chrUn_gl000245 LN:36651 > > @SQ SN:chrUn_gl000246 LN:38154 > > @SQ SN:chrUn_gl000247 LN:36422 > > @SQ SN:chrUn_gl000248 LN:39786 > > @SQ SN:chrUn_gl000249 LN:38502 > > seq.13657392b 147 chr1 659743 255 17S79M301N5M = 659609 -518 CCCGTCCCACACTTGTATCAGTCTCTTGACGCGGCCCTGGCTGCCCGACCACTTCTTCTGCCCGAGATTCACGTGAGGCTGAGAGTAGGGGCAGGGCCAGC [MUUM^YWJ^LZ\UQeeeeUeUeff]bbcBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB OL:A:F IH:i:2 HI:i:2 > > seq.30737805a 83 chr1 660031 255 40M3D61M = 659891 243 TGGGGCAGCATGGGCAGGATGTTCTGCACACAAACCTTGGAGAAGATGTGTGCATAGCGGGTCCACTGCTGCTGCCCCTGCCCTGACTCCCAGCCCTGCCT gggggggggggggggggggggdfggggebgcgebddadeadfac`Xa`a`dedddb__gddbddcae\dd\_X_bccb^eggaee_abcebaBBBBBBBBB OL:A:F IH:i:11 HI:i:8 > > ------------------------------------------------------------------------------ > > Protect Your Site and Customers from Malware Attacks > > Learn about various malware tactics and how to avoid them. Understand > > malware threats, the impact they can have on your business, and how you > > can protect your company and customers by using code signing. > > http://p.sf.net/sfu/oracle-sfdevnl_______________________________________________ > > Samtools-help mailing list > > Sam...@li... > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |