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In memory one off #2

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merged 31 commits into from
Mar 21, 2022
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0774b7e
expose an in-mem one_off
wasade Mar 11, 2022
3efe505
load from scipy.sparse like data
wasade Mar 12, 2022
114591c
comment on from scipy.sparse
wasade Mar 12, 2022
8663ed6
use biom not biom_interface
wasade Mar 12, 2022
e9e5b36
limit one_off_inmem to c++
wasade Mar 14, 2022
cebd37b
do not extern inmem c-style
wasade Mar 14, 2022
6fcfb16
Bring over a few additional headers
wasade Mar 14, 2022
26aa816
add nullary constructors
wasade Mar 15, 2022
4def03f
more conservative destructor, use pointers
wasade Mar 15, 2022
1ca1215
Actually copy the ids
wasade Mar 15, 2022
c5056b1
address many of @sfiligoi's comments
wasade Mar 16, 2022
47c579e
nearly there
wasade Mar 16, 2022
919956e
close...
wasade Mar 16, 2022
de83beb
use reserve rather than resize
wasade Mar 16, 2022
66a09e3
kick ci
wasade Mar 16, 2022
e8a8fa0
move status enums to their own header
wasade Mar 16, 2022
e192e9a
define in situ
wasade Mar 16, 2022
01f1d67
remove unnecessary includes
wasade Mar 16, 2022
f35eac2
Address @sfiligoi's comments
wasade Mar 16, 2022
3059f2a
remove commted out function
wasade Mar 16, 2022
d103920
EXTERN on a few support methods
wasade Mar 16, 2022
88bc35c
sync declaration
wasade Mar 16, 2022
aa9523d
omp pragmas
wasade Mar 17, 2022
044fe19
parallelize get_sample_counts
wasade Mar 17, 2022
d53283a
remove much of one level of copying
wasade Mar 18, 2022
f2826d1
inmem now full matrix, and fix input types for biom
wasade Mar 18, 2022
f37912b
minor change to resize and some parallel w/ bptree
wasade Mar 18, 2022
0f98a90
remove unneeded parallels
wasade Mar 19, 2022
0252938
Allow the caller to allocate results
wasade Mar 21, 2022
4f1ab8a
partial maybe is sensitive
wasade Mar 21, 2022
80aeab0
Addressing @sfiligoi's comments
wasade Mar 21, 2022
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remove commted out function
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wasade committed Mar 16, 2022
commit 3059f2a80474fffc8169cf559d1cfa264c466f20
6 changes: 0 additions & 6 deletions src/api.hpp
Original file line number Diff line number Diff line change
Expand Up @@ -208,12 +208,6 @@ EXTERN ComputeStatus one_off_inmem(support_biom_t *table_data, support_bptree_t
const char* unifrac_method, bool variance_adjust, double alpha,
bool bypass_tips, unsigned int threads, mat_t** result);

/* define this thing... */

//compute_status one_off_inmem_cpp(su::biom &table, su::BPTree &tree,
// const char* unifrac_method, bool variance_adjust, double alpha,
// bool bypass_tips, unsigned int nthreads, mat_t** result);

/* Compute UniFrac - matrix form
*
* biom_filename <const char*> the filename to the biom table.
Expand Down