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Various commentaries and insignificant fixes

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This commit is contained in:
Celine Mercier
2019-01-21 17:32:44 +01:00
parent c7f5b8d980
commit 0b62619e4e
4 changed files with 7 additions and 5 deletions
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1
python/obitools3/utils.pxd
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@ -2,6 +2,7 @@
from obitools3.dms.capi.obitypes cimport obitype_t, index_t from obitools3.dms.capi.obitypes cimport obitype_t, index_t
cdef obi_errno_to_exception(int obi_errno, index_t line_nb=*, object elt_id=*, str error_message=*) cdef obi_errno_to_exception(int obi_errno, index_t line_nb=*, object elt_id=*, str error_message=*)
cdef bytes str2bytes(str string) cdef bytes str2bytes(str string)

2
python/obitools3/utils.pyx
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@ -17,8 +17,6 @@ from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \
import re import re
#from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored
# TODO RollbackException? # TODO RollbackException?
cdef obi_errno_to_exception(int obi_errno, index_t line_nb=-1, object elt_id=None, str error_message=None) : cdef obi_errno_to_exception(int obi_errno, index_t line_nb=-1, object elt_id=None, str error_message=None) :

2
src/obi_ecopcr.c
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@ -359,6 +359,8 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
int32_t i; int32_t i;
// TODO add check for primer longer than MAX_PAT_LEN (32)
ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides; ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides;
rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides; rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides;

5
src/obidmscolumn.c
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@ -1351,8 +1351,9 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
column->writable = false; column->writable = false;
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is opened // If the data type is OBI_STR, OBI_SEQ or OBI_QUAL or the column contains tuples, the associated indexer is opened
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL)) // TODO maybe store a 'indexer' bool in the header instead
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL) || ((column->header)->tuples))
{ {
column->indexer = obi_open_indexer(dms, (column->header)->indexer_name); column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
if (column->indexer == NULL) if (column->indexer == NULL)