htslib
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samtools
C library for high-throughput sequencing data formats
We are utilizing EMC on-premise s3-compatible storage. Htslib does not accommodate non (.s3.amazonaws.com) endpoint urls. We can successfully modify, re-compile and use htslib/samtools if we swap in our own endpoint...
I would like to point out that identifiers like “[`_CRAM_SAMTOOLS_H_`](https://github.com/samtools/htslib/blob/5d114ebd8e9b80622769b8e575c5a9359cd51273/cram/cram_samtools.h#L31 "Update candidate")” and “[`_AC_KLIST_H`](https://github.com/samtools/htslib/blob/bf753361dab9b1640cf64f7886dbfe35357a43c5/htslib/klist.h#L26 "Another update candidate")” [do not fit](https://www.securecoding.cert.org/confluence/display/c/DCL37-C.+Do+not+declare+or+define+a+reserved+identifier#DCL37-C.Donotdeclareordefineareservedidentifier-NoncompliantCodeExample%28HeaderGuard%29 "Do not use identifiers which are reserved for the compiler...
Hi! I wonder if it's possible to implement a "peek" mode for tabix query, such that one can quickly get the amount of data within a genomic interval from an...
If the BAQ calculation is a significant compute fraction of a variant calling pipeline can we get a faster turnaround by threading that BAQ calculation? (be it in `samtools calmd`,...
This is a reminder for me to discuss whether we should enforce checks of return codes. Just encountered a nasty case of big truncated data, probably preventable if the chief...
This pull request extracts the function `m5_to_ref` from `cram_io` and adds tests. `m5_to_ref` and helper functions for it are added in a new file called `ref.c`. I've also added a...
The eventual use of this PR will be to replace the reference file wrapper in the reference fetching logic from an `mFILE` to an mmapped hFILE. This will eventually be...
How do you test whether you are at the end of an `hFILE`? The simplest way I could come up is the following: ``` if ( hgetc(fp) != EOF )...
some minor optimizations : in `sam.c / sam_format1` I replaced the successions of `if/then` with `switch/case`. replaced the `goto` with a macro. I also fixed a | FIXME` in the...
…ewline character in SAM header.
