biobambam2
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gt1
Tools for early stage alignment file processing
In the readme you indicate the REF_PATH/REF_CACHE variables are used for cram output. https://github.com/gt1/biobambam2#bamsormadup-and-cram-output Can you clarify if they are used when reading CRAM as well? When receiving data from...
I installed libmaus2 in my home directory ~/include/libmaus2 ~/lib$ ls libmaus* libmaus2.a libmaus2.la libmaus2_simd_align_128.so.2 libmaus2_simd_align_256.so.2 libmaus2digests.a libmaus2seqchksumsfactory.a libmaus2_simd_align_128.so.2.0.499 libmaus2_simd_align_256.so.2.0.499 libmaus2digests_sse4.a libmaus2_simd_align_128.a libmaus2_simd_align_256.a libmaus2.so libmaus2fftw.a libmaus2_simd_align_128.la libmaus2_simd_align_256.la libmaus2.so.2 libmaus2_irods.a libmaus2_simd_align_128.so libmaus2_simd_align_256.so...
Hi, Would it be possible to add a flag to filter for mapping quality to bamsormadup? This would make it a one stop application for all our bam processing needs....
Hi German, please improve the error message and print out the wrong readname. ``` bamsort SO=coordinate inputthreads=10 outputthreads=10 level=9 index=1 O=foo.refsorted.bam I=foo.bam [V] Reading alignments from source. Invalid alignment: Query...
Hi, current git master checkout crashes for me (well even previous versions). ``` repository: https://github.com/gt1/libmaus2.git at the commit: 694c2180076cd5986fea0532b057065f905d49b5 repository: https://github.com/gt1/biobambam2.git at the commit: 5798e74558e001e33855cb93cc8bf149344b931d ``` ``` LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE==1m export LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE...
Hi, I find it unusual that bamsort, bammerge and probably many other utils crash if they are executed without an argument. Please assume '-h' was passed to the utility and...
Hi, time to time bamsort gets stuck while reading input data. At other times a `top` program output is logged as the last one in logfile and bamsort keeps running...
Dear biobambam2 team, bamsort fails if the @PG header is malformed. In my case, the @PG line is missing the word "ID:" after processing the BAM file with another tool....
Hi, biobambam2 currently only supports position values up to 2^29 (= 536,870,912). The BAM specification allows for position values up to 2^31 (=2,147,483,648 ) See page 5, section 1.4 The...
German; @ameynert reported an issue using bamsormadup for a deep WGS sample within bcbio. We're running bamcat and bamsormadup on a split set of alignment BAMs to generate a final...
