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small fixes and improvements

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This commit is contained in:
mercierc
2021-11-11 15:26:09 +13:00
parent f6353fbf28
commit 53b3d81137
2 changed files with 5 additions and 3 deletions
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2
python/obitools3/commands/grep.pyx
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@ -91,7 +91,7 @@ def addOptions(parser):
metavar="<ATTRIBUTE_NAME>", metavar="<ATTRIBUTE_NAME>",
help="Select records with the attribute <ATTRIBUTE_NAME> " help="Select records with the attribute <ATTRIBUTE_NAME> "
"defined (not set to NA value). " "defined (not set to NA value). "
"Several -a options can be used on the same " "Several -A options can be used on the same "
"command line.") "command line.")
group.add_argument("-L", "--lmax", group.add_argument("-L", "--lmax",

6
src/build_reference_db.c
View File

@ -77,6 +77,7 @@ static inline ecotx_t* get_lca_from_merged_taxids(Obiview_p view, OBIDMS_column_
{ {
ecotx_t* taxon = NULL; ecotx_t* taxon = NULL;
ecotx_t* lca = NULL; ecotx_t* lca = NULL;
ecotx_t* lca1 = NULL;
int32_t taxid; int32_t taxid;
index_t taxid_idx; index_t taxid_idx;
int64_t taxid_str_idx; int64_t taxid_str_idx;
@ -108,10 +109,11 @@ static inline ecotx_t* get_lca_from_merged_taxids(Obiview_p view, OBIDMS_column_
else else
{ {
// Compute LCA // Compute LCA
lca1 = lca;
lca = obi_taxo_get_lca(taxon, lca); lca = obi_taxo_get_lca(taxon, lca);
if (lca == NULL) if (lca == NULL)
{ {
obidebug(1, "\nError getting the last common ancestor of two taxa when building a reference database"); obidebug(1, "\nError getting the last common ancestor of two taxa when building a reference database, %d %d", taxid, lca1->taxid);
return NULL; return NULL;
} }
} }
@ -185,7 +187,7 @@ int build_reference_db(const char* dms_name,
matrix_view_name = strcpy(matrix_view_name, o_view_name); matrix_view_name = strcpy(matrix_view_name, o_view_name);
strcat(matrix_view_name, "_matrix"); strcat(matrix_view_name, "_matrix");
fprintf(stderr, "Aligning queries with reference database...\n"); fprintf(stderr, "Aligning sequences...\n");
if (obi_lcs_align_one_column(dms_name, if (obi_lcs_align_one_column(dms_name,
refs_view_name, refs_view_name,
"", "",