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Wrapping htslib #79

Merged
merged 20 commits into from
Jul 28, 2023
Merged

Wrapping htslib #79

merged 20 commits into from
Jul 28, 2023

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andrewdavidsmith
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Wrapping htslib so that app sources do not need to deal directly with bam1_t structs, with samFile or with hts_tpool and these can be used with RAII.

@andrewdavidsmith
Adding some files with helper code to interface between the htslib an…
d9cddfa 
…d the c++
@andrewdavidsmith
Adding dependency on bamxx files for testing modifications to dnmtools
6ae24ca
@andrewdavidsmith
format-reads: setup for using the bamxx sources
c1f841c
@andrewdavidsmith
bug in dnmt_error.hpp: is is using ostringstream but not including th…
cc3e57b 
…e necessary header
@andrewdavidsmith
Building libbamxx.a as a library because it seems more convenient for…
8383bac 
… now
@andrewdavidsmith
Adding all the includes from bamxx so that apps won't need to
26a2dab
@andrewdavidsmith
Move changes to remove direct use of htslib functions
1ea5aec
@andrewdavidsmith
Updated uniq.cpp to remove the direct use of htslib functions
8a1d886
@andrewdavidsmith
Adding a check for the input file existing before attempting to deduc…
b216eef 
…e if it is a mapped reads file
@andrewdavidsmith
Removing bamxx as a library and just using the header for now
1acaeb8
@andrewdavidsmith
Updates after finding performance issues.
12c70a0
@andrewdavidsmith
Moved code in from uniq.cpp and using the header for the accessors of…
1b27d43 
… bam_rec structs for now
@andrewdavidsmith
uniq.cpp: updated how bam_rec etc are used and moved some of the code…
8c0082b 
… that needs bam1_t internals to bam_record_utils.hpp
@andrewdavidsmith
Removing commonly used macros and replacing them with hopefully zero …
8845459 
…cost functions
@andrewdavidsmith
Using more functions from bam_record_utils to avoid the bam1_t in mor…
d09067b 
…e places and the macros
@andrewdavidsmith
Adding bam_record.hpp as interface into the htslib stuff
6777fa9
@andrewdavidsmith
bam_record_utils: Removed some commented out code and more direct use…
b156f96 
… of pointers
@andrewdavidsmith
Adding bam_record.hpp directly in common
b215b78
@andrewdavidsmith
Merging with master
004bb43
@andrewdavidsmith
Makefile.am: Adding forgotten bam_record.hpp
02fff6f
@masarunakajima masarunakajima merged commit 45e54b0 into master Jul 28, 2023
1 check passed
@masarunakajima masarunakajima deleted the wrapping_htslib branch July 28, 2023 23:14
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@masarunakajima masarunakajima Awaiting requested review from masarunakajima

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@andrewdavidsmith @masarunakajima