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ecopcr: fixed and improved the options to keep nuclotides around the

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amplicon
This commit is contained in:
Celine Mercier
2019-12-26 20:45:54 +01:00
parent 694d1934a8
commit 6c018b403c
5 changed files with 28 additions and 16 deletions
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22
src/obi_ecopcr.c
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@ -77,7 +77,8 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode);
* @param err2 The number of errors in the second primer.
* @param strand The DNA strand direction of the amplicon (R(everse) or D(irect)).
* @param kingdom_mode Whether the kingdom or the superkingdom informations should be printed to the output.
* @param keep_nucleotides Number of nucleotides kept on each side of the amplicon.
* @param keep_nucleotides Number of nucleotides kept on each side of the amplicon (not including the primers if they are kept).
* @param keep_primers Whether to keep the primers.
* @param i_id_column A pointer on the input sequence identifier column.
* @param o_id_column A pointer on the output sequence identifier column.
* @param o_ori_seq_len_column A pointer on the original sequence length column.
@ -124,6 +125,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
int32_t err1, int32_t err2,
char strand, bool kingdom_mode,
int keep_nucleotides,
bool keep_primers,
OBIDMS_column_p i_id_column, OBIDMS_column_p o_id_column, OBIDMS_column_p o_ori_seq_len_column,
OBIDMS_column_p o_amplicon_column, OBIDMS_column_p o_amplicon_length_column,
OBIDMS_column_p o_taxid_column, OBIDMS_column_p o_rank_column, OBIDMS_column_p o_name_column,
@ -328,6 +330,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
int32_t err1, int32_t err2,
char strand, bool kingdom_mode,
int keep_nucleotides,
bool keep_primers,
OBIDMS_column_p i_id_column, OBIDMS_column_p o_id_column, OBIDMS_column_p o_ori_seq_len_column,
OBIDMS_column_p o_amplicon_column, OBIDMS_column_p o_amplicon_length_column,
OBIDMS_column_p o_taxid_column, OBIDMS_column_p o_rank_column, OBIDMS_column_p o_name_column,
@ -382,7 +385,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
oligo2[o1->patlen] = 0;
error2 = err1;
if (keep_nucleotides == 0)
if (!keep_primers)
amplicon+=o2->patlen;
else
{
@ -401,7 +404,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
oligo2[o2->patlen] = 0;
error2 = err2;
if (keep_nucleotides==0)
if (!keep_primers)
amplicon+=o1->patlen;
else
{
@ -411,16 +414,11 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
}
ecoComplementSequence(oligo2);
if (keep_nucleotides == 0)
if (!keep_primers)
amplicon[amplicon_len]=0;
else
{
amplicon_len = ldelta+rdelta+amplicon_len;
for (i=0; i<ldelta; i++)
amplicon[i]|=32;
for (i=1; i<=rdelta; i++)
amplicon[amplicon_len-i]|=32;
amplicon[amplicon_len] = 0;
}
@ -659,6 +657,7 @@ int obi_ecopcr(const char* i_dms_name,
double salt,
int saltmethod,
int keep_nucleotides,
bool keep_primers,
bool kingdom_mode)
{
@ -717,6 +716,9 @@ int obi_ecopcr(const char* i_dms_name,
signal(SIGINT, sig_handler);
if (keep_nucleotides > 0)
keep_primers = true;
if (circular)
{
circular = strlen(primer1);
@ -1076,6 +1078,7 @@ int obi_ecopcr(const char* i_dms_name,
erri, errj,
'D', kingdom_mode,
keep_nucleotides,
keep_primers,
i_id_column, o_id_column, o_ori_seq_len_column,
o_amplicon_column, o_amplicon_length_column,
o_taxid_column, o_rank_column, o_name_column,
@ -1163,6 +1166,7 @@ int obi_ecopcr(const char* i_dms_name,
erri, errj,
'R', kingdom_mode,
keep_nucleotides,
keep_primers,
i_id_column, o_id_column, o_ori_seq_len_column,
o_amplicon_column, o_amplicon_length_column,
o_taxid_column, o_rank_column, o_name_column,