samtools mpileup fails if .bam are differently ordered / headers are different

[lpryszcz]

I have two .bam files from Encode: ENCFF879HJE and ENCFF731VMU. They were sorted by different algorithms, thus chromosome order / headers are slightly different.
First command fails with Segmentation fault (core dumped) and exit code 139, while second works fine. Why is that?

samtools mpileup -r chr1:249230621 ENCFF879HJE.bam ENCFF731VMU.bam > /dev/null
samtools mpileup -r chr1:249230621 ENCFF731VMU.bam ENCFF879HJE.bam > /dev/null

Theirs headers are as follows:

• ENCFF879HJE.bam

@HD     VN:1.4  SO:coordinate
@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:chr1 LN:249250621
@SQ     SN:chr20        LN:63025520
@SQ     SN:chr21        LN:48129895
@SQ     SN:chr22        LN:51304566
@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:chrM LN:16571
@SQ     SN:chrX LN:155270560
@SQ     SN:chrY LN:59373566
@PG     ID:bwa  PN:bwa  VN:0.7.12-r1039 CL:bwa sampe -n 10 -a 750 /net/lebowski/vol2/solexa_genomes/illumina/Homo_sapiens/UCSC/hg19/genom
e-sets/bwa-0.7.0/hg19 /tmp/3948300.1.all.q/R1.sai /tmp/3948300.1.all.q/R2.sai /tmp/3948300.1.all.q/trimmed.R1.fastq.gz /tmp/3948300.1.all
.q/trimmed.R2.fastq.gz
...

• ENCFF731VMU.bam

@HD     VN:1.4  SO:coordinate
@SQ     SN:ERCC-00002   LN:1061
...
@SQ     SN:ERCC-00171   LN:505
@SQ     SN:chr1 LN:249250621
@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:chr2 LN:243199373
@SQ     SN:chr20        LN:63025520
@SQ     SN:chr21        LN:48129895
@SQ     SN:chr22        LN:51304566
@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:chrM LN:16571
@SQ     SN:chrX LN:155270560
@SQ     SN:chrY LN:59373566
@PG     ID:Samtools     PN:Samtools     CL:perl tophat_bam_xsA_tag_fix.pl tophat_out/accepted_hits.bam | samtools view -bS - | samtools sort - mapped_fixed; samtools merge -h newHeader.sam merged.bam mapped_fixed.bam out/unmapped.bam        PP:Tophat       VN:VN:0.1.17 (r973:277)
...

[pd3]

Hi, this is a known issue, the program makes this simplifying assumption about the sequences being the same and in the same order. It is one of the things on the to do list that never became a priority and has been waiting for the header parsing API. At this time the only solution is to reorder, sorry!