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Multi-threading bug in cram/htslib #265

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jkbonfield opened this issue Sep 7, 2015 · 0 comments
Closed

Multi-threading bug in cram/htslib #265

jkbonfield opened this issue Sep 7, 2015 · 0 comments
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Something for me to investigate alas.

@ seq3a[scratch01/jkb]; ./samtools flagstat --input-fmt-option nthreads=1 _fail.cram
Read has alignment position 0 but no unmapped flag
Failure to decode slice
[bam_flagstat_core] Truncated file? Continue anyway.
98644678 + 0 in total (QC-passed reads + QC-failed reads)
12609659 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
98644678 + 0 mapped (100.00% : N/A)
86035019 + 0 paired in sequencing
43667265 + 0 read1
42367754 + 0 read2
6255890 + 0 properly paired (7.27% : N/A)
80610698 + 0 with itself and mate mapped
5424321 + 0 singletons (6.30% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

vs

@ seq3a[scratch01/jkb]; ./samtools flagstat --input-fmt-option nthreads=8 _fail.cram
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Read has alignment position 0 but no unmapped flag
Segmentation fault (core dumped)

Helgrind currently churning. Joy!
@jkbonfield jkbonfield self-assigned this Sep 7, 2015
pd3 pushed a commit to pd3/htslib that referenced this issue Sep 25, 2015
@mcshane
Merge pull request samtools#265 from samtools/feature/norm-set-ref
dbb7dda 
bcftools norm set REF allele
charles-plessy added a commit to Debian/htslib that referenced this issue Dec 24, 2015
@charles-plessy
Merge tag '1.3' into debian/unstable
68e6f6c 
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes

* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
  and FTP, when HTSlib is configured to use libcurl for network file access
  rather than the included basic knetfile networking.

* HTSlib can be built to use remote access hFILE backends (such as iRODS
  and libcurl) via a plugin mechanism.  This allows other backends to be
  easily added and facilitates building tools that use HTSlib, as they
  don't need to be linked with the backends' various required libraries.

* fai_build() and samtools faidx now accept initial whitespace in ">"
  headers (e.g., "> chr1 description" is taken to refer to "chr1").

* tabix --only-header works again (was broken in 1.2.x; samtools#249).

* HTSlib's configure script and Makefile now fully support the standard
  convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
  as needed.  Previously the Makefile listened to $(LDLIBS) instead; if you
  were overriding that, you should now override LIBS rather than LDLIBS.

* Fixed bugs samtools#168, samtools#172, samtools#176, samtools#197, samtools#206, samtools#225, samtools#245, samtools#265, samtools#295, and samtools#296.
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