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Added signal catching and handling in C and Cython

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This commit is contained in:
Celine Mercier
2019-09-21 16:47:22 +02:00
parent 06f9d6da60
commit ec0737a600
23 changed files with 178 additions and 25 deletions
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11
src/obi_lcs.c
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@ -21,6 +21,7 @@
#include "obi_lcs.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "sse_banded_LCS_alignment.h"
@ -428,6 +429,8 @@ int obi_lcs_align_one_column(const char* dms_name,
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
signal(SIGINT, sig_handler);
k = 0;
// Open DMS
@ -574,6 +577,9 @@ int obi_lcs_align_one_column(const char* dms_name,
if (i%100 == 0)
fprintf(stderr,"\rDone : %f %% ", (i / (float) seq_count)*100);
if (! keep_running)
return -1;
// Get first id idx
id1_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq_view, id_column, i, 0); // TODO Could there be multiple IDs per line?
// Get first sequence and its index
@ -725,6 +731,8 @@ int obi_lcs_align_two_columns(const char* dms_name,
OBIDMS_column_p ali_length_column = NULL;
OBIDMS_column_p score_column = NULL;
signal(SIGINT, sig_handler);
k = 0;
// Open DMS
@ -979,6 +987,9 @@ int obi_lcs_align_two_columns(const char* dms_name,
for (j=0; j < seq2_count; j++)
{
if (! keep_running)
return -1;
// Get second sequence and its index
seq2_idx = obi_get_index_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);
blob2 = obi_get_blob_with_elt_idx_and_col_p_in_view(seq2_view, i_seq2_column, j, seq2_elt_idx);