[med-svn] [gmap] 02/04: Imported Upstream version 2015-12-31.v7
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Feb 5 15:21:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 108926cde9abc21780fab8e244044383bec55381
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Feb 5 10:35:21 2016 +0100
Imported Upstream version 2015-12-31.v7
---
ChangeLog | 7 ++
src/output.c | 19 +++--
src/samprint.c | 256 ++++++++++++++++++++++++++++++---------------------------
src/samprint.h | 10 +--
src/stage2.c | 4 +-
5 files changed, 159 insertions(+), 137 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index cb8f107..c2032b1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+2016-02-04 twu
+
+ * stage2.c: Fixed termination condition for while loop
+
+ * output.c, samprint.c, samprint.h: Added check for artificial mate in
+ --add-paired-nomappers mode, to set SAM flag correctly
+
2016-01-21 twu
* dynprog_genome.c: Fixed bug in checking bestrL before it is computed,
diff --git a/src/output.c b/src/output.c
index 3b59563..4afafef 100644
--- a/src/output.c
+++ b/src/output.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: output.c 181903 2016-01-07 20:30:55Z twu $";
+static char rcsid[] = "$Id: output.c 183725 2016-02-04 00:40:15Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -186,7 +186,8 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
SAM_print_nomapping(fp,ABBREV_NOMAPPING_1,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,/*npaths_mate*/0,/*mate_chrpos*/0U,
+ /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,
+ /*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
Shortread_print_query_singleend(*fp_failedinput_1,queryseq1,/*headerseq*/queryseq1);
@@ -221,7 +222,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/0,quality_shift,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
@@ -237,7 +238,8 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
SAM_print_nomapping(fp,ABBREV_UNPAIRED_TRANSLOC,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,/*npaths_mate*/0,/*mate_chrpos*/0U,
+ /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
Shortread_print_query_singleend(*fp_failedinput_1,queryseq1,/*headerseq*/queryseq1);
@@ -262,7 +264,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/0,quality_shift,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
@@ -279,7 +281,8 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
SAM_print_nomapping(fp,ABBREV_UNPAIRED_MULT_XS,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,/*npaths_mate*/0,/*mate_chrpos*/0U,
+ /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
Shortread_print_query_singleend(*fp_failedinput_1,queryseq1,/*headerseq*/queryseq1);
@@ -304,7 +307,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/0,quality_shift,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
@@ -754,7 +757,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
Sequence_print_header(fp,headerseq,checksump);
if (npaths == 0) {
- print_npaths(fp,0,chrsubset_name,
+ print_npaths(fp,/*npaths*/0,chrsubset_name,
/*mergedp*/false,/*chimera*/NULL,Result_failuretype(result));
diff --git a/src/samprint.c b/src/samprint.c
index 2fe012c..221dd1d 100644
--- a/src/samprint.c
+++ b/src/samprint.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: samprint.c 181904 2016-01-07 20:31:34Z twu $";
+static char rcsid[] = "$Id: samprint.c 183725 2016-02-04 00:40:15Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -109,7 +109,7 @@ SAM_setup (bool add_paired_nomappers_p_in, bool paired_flag_means_concordant_p_i
unsigned int
SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
- bool first_read_p, int pathnum, int npaths, int npaths_mate,
+ bool first_read_p, int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
int absmq_score, int first_absmq, bool invertp, bool invert_mate_p) {
unsigned int flag = 0U;
@@ -136,7 +136,11 @@ SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
debug(printf("SECOND_READ %d\n",SECOND_READ_P));
flag |= SECOND_READ_P;
}
- if (npaths_mate == 0) {
+ if (artificial_mate_p == true) {
+ debug(printf("MATE_UNMAPPED %d\n",MATE_UNMAPPED));
+ flag |= MATE_UNMAPPED;
+
+ } else if (npaths_mate == 0) {
debug(printf("MATE_UNMAPPED %d\n",MATE_UNMAPPED));
flag |= MATE_UNMAPPED;
@@ -202,7 +206,7 @@ SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
debug(printf("NOT_PRIMARY %d\n",NOT_PRIMARY));
flag |= NOT_PRIMARY;
} else {
- /* Just as good as first alignment, so don't mark as secondary */
+ /* Just as good as first alignment, so don't mark as altloc */
}
}
@@ -355,8 +359,8 @@ make_complement_buffered (char *complement, char *sequence, unsigned int length)
void
SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3end_T mate, char *acc1, char *acc2,
Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p,
- int pathnum, int npaths, int npaths_mate, Chrpos_T mate_chrpos, int quality_shift,
- char *sam_read_group_id, bool invertp, bool invert_mate_p) {
+ int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
+ Chrpos_T mate_chrpos, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p) {
unsigned int flag;
@@ -373,7 +377,7 @@ SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3
/* 5. MAPQ: Mapping quality. Picard says MAPQ should be 0 for an unmapped read */
/* 6. CIGAR */
flag = SAM_compute_flag(/*plusp (NA)*/true,mate,resulttype,first_read_p,
- /*pathnum*/0,/*npaths*/0,npaths_mate,
+ /*pathnum*/0,/*npaths*/0,artificial_mate_p,npaths_mate,
/*absmq_score*/0,/*first_absmq*/0,invertp,invert_mate_p);
FPRINTF(fp,"\t%u\t*\t0\t0\t*",flag);
@@ -1166,7 +1170,7 @@ print_substrings (Filestring_T fp, char *abbrev, Stage3end_T stage3end, Stage3en
int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Shortread_T queryseq, int pairedlength,
Chrpos_T chrpos, Chrpos_T mate_chrpos, int hardclip_low, int hardclip_high,
- Resulttype_T resulttype, bool first_read_p, int npaths_mate,
+ Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool circularp) {
unsigned int flag = 0U;
@@ -1209,8 +1213,8 @@ print_substrings (Filestring_T fp, char *abbrev, Stage3end_T stage3end, Stage3en
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,npaths_mate,absmq_score,first_absmq,
- invertp,invert_mate_p);
+ pathnum,npaths,artificial_mate_p,npaths_mate,
+ absmq_score,first_absmq,invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
/* 3. RNAME: chr */
@@ -2170,7 +2174,8 @@ print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T t
char *acc1, char *acc2, int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
Chrpos_T concordant_chrpos, Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
- int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p, int npaths_mate,
+ int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p,
+ bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool use_hardclip_p, bool print_xt_p, int donor_sensedir, char donor_strand, char acceptor_strand,
char *donor_chr, char *acceptor_chr, char donor1, char donor2, char acceptor2, char acceptor1,
@@ -2202,7 +2207,7 @@ print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T t
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,npaths_mate,absmq_score,first_absmq,
+ pathnum,npaths,artificial_mate_p,npaths_mate,absmq_score,first_absmq,
invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
@@ -2685,7 +2690,7 @@ print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3e
char *acc1, char *acc2, int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
Chrpos_T concordant_chrpos, Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
- int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p, int npaths_mate,
+ int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool use_hardclip_p, bool print_xt_p, int acceptor_sensedir, char donor_strand, char acceptor_strand,
char *donor_chr, char *acceptor_chr, char donor1, char donor2, char acceptor2, char acceptor1,
@@ -2717,7 +2722,7 @@ print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3e
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,npaths_mate,absmq_score,first_absmq,
+ pathnum,npaths,artificial_mate_p,npaths_mate,absmq_score,first_absmq,
invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
@@ -3193,7 +3198,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
Chrpos_T mate_chrpos, int hardclip_low, int hardclip_high,
- Resulttype_T resulttype, bool first_read_p, int npaths_mate,
+ Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p) {
Chrpos_T donor_chrpos, acceptor_chrpos, concordant_chrpos;
Substring_T donor, acceptor;
@@ -3271,7 +3276,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3281,7 +3286,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3292,7 +3297,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3305,7 +3310,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3315,7 +3320,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3326,7 +3331,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3340,7 +3345,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3350,7 +3355,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3361,7 +3366,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3374,7 +3379,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3384,7 +3389,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3395,7 +3400,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3410,7 +3415,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3420,7 +3425,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3431,7 +3436,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3444,7 +3449,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3454,7 +3459,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
/*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3465,7 +3470,7 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
chromosome_iit,queryseq,pairedlength,
concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
@@ -3489,8 +3494,8 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
Shortread_T queryseq_mate, int pairedlength, Chrpos_T chrpos, Chrpos_T mate_chrpos,
int clipdir, int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
- Resulttype_T resulttype, bool first_read_p,
- int npaths_mate, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
+ Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
+ int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool merge_samechr_p) {
Hittype_T hittype;
unsigned int flag;
@@ -3504,8 +3509,8 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
/* Also, can use this test here because --quiet-if-excessive cases go directly to SAM_print_nomapping */
if (npaths == 0) {
SAM_print_nomapping(fp,abbrev,queryseq,mate,acc1,acc2,chromosome_iit,resulttype,first_read_p,
- /*pathnum*/0,/*npaths*/0,npaths_mate,mate_chrpos,quality_shift,
- sam_read_group_id,invertp,invert_mate_p);
+ /*pathnum*/0,/*npaths*/0,artificial_mate_p,npaths_mate,mate_chrpos,
+ quality_shift,sam_read_group_id,invertp,invert_mate_p);
if (fp_failedinput != NULL) {
if (first_read_p == true) {
@@ -3537,8 +3542,8 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
}
flag = SAM_compute_flag(Stage3end_plusp(this),mate,resulttype,first_read_p,
- pathnum,npaths,npaths_mate,absmq_score,first_absmq,
- invertp,invert_mate_p);
+ pathnum,npaths,artificial_mate_p,npaths_mate,
+ absmq_score,first_absmq,invertp,invert_mate_p);
querylength = Shortread_fulllength(queryseq);
if ((circularpos = Stage3end_circularpos(this)) > 0
@@ -3614,13 +3619,13 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,chromosome_iit,queryseq,pairedlength,
mate_chrpos,hardclip5_low,hardclip5_high,resulttype,/*first_read_p*/true,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p);
} else {
print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,chromosome_iit,queryseq,pairedlength,
mate_chrpos,hardclip3_low,hardclip3_high,resulttype,/*first_read_p*/false,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p);
}
@@ -3635,24 +3640,24 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/true);
print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
/*chrpos*/1,mate_chrpos,/*hardclip_low*/circularpos,/*hardclip_high*/0,
- resulttype,first_read_p,npaths_mate,quality_shift,sam_read_group_id,
+ resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/true);
} else if (first_read_p == true) {
print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,hardclip5_low,hardclip5_high,resulttype,/*first_read_p*/true,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/false);
} else {
print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,hardclip3_low,hardclip3_high,resulttype,/*first_read_p*/false,
- npaths_mate,quality_shift,sam_read_group_id,
+ artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/false);
}
}
@@ -3696,12 +3701,14 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Filestring_set_split_output(fp,OUTPUT_NM);
SAM_print_nomapping(fp,ABBREV_NOMAPPING_1,queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,/*npaths_mate*/0,
+ /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,
+ /*artificial_mate_p*/false,/*npaths_mate*/0,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_NOMAPPING_2,queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/0,/*npaths*/0,/*npaths_mate*/0,
+ /*first_read_p*/false,/*pathnum*/0,/*npaths*/0,
+ /*artificial_mate_p*/false,/*npaths_mate*/0,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -3754,7 +3761,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
@@ -3766,7 +3773,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
@@ -3785,7 +3792,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
}
/* merging changes resulttype from UNPAIRED_UNIQ to SINGLEEND_UNIQ */
flag = SAM_compute_flag(Stage3end_plusp(hit5),/*mate*/NULL,/*resulttype*/SINGLEEND_UNIQ,/*first_read_p*/true,
- /*pathnum*/1,/*npaths*/1,/*npaths_mate*/0,
+ /*pathnum*/1,/*npaths*/1,/*artificial_mate_p*/false,/*npaths_mate*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*invertp*/false,
/*invert_mate_p*/false);
Filestring_set_split_output(fp,OUTPUT_UU);
@@ -3823,15 +3830,15 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
SAM_print_nomapping(fp,ABBREV_CONCORDANT_TRANSLOC,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
- /*mate_chrpos*/0U,quality_shift,
- sam_read_group_id,invert_first_p,invert_second_p);
+ /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,/*mate_chrpos*/0U,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_CONCORDANT_TRANSLOC,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
- /*mate_chrpos*/0U,quality_shift,
- sam_read_group_id,invert_second_p,invert_first_p);
+ /*first_read_p*/false,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,/*mate_chrpos*/0U,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
} else {
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
@@ -3868,7 +3875,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
@@ -3880,7 +3887,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
}
@@ -3895,13 +3902,15 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
SAM_print_nomapping(fp,ABBREV_CONCORDANT_MULT_XS,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_CONCORDANT_MULT_XS,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
+ /*first_read_p*/false,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -3946,7 +3955,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
@@ -3958,7 +3967,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
@@ -3977,7 +3986,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
}
/* merging changes resulttype from UNPAIRED_UNIQ to SINGLEEND_UNIQ */
flag = SAM_compute_flag(Stage3end_plusp(hit5),/*mate*/NULL,/*resulttype*/SINGLEEND_UNIQ,/*first_read_p*/true,
- /*pathnum*/1,/*npaths*/1,/*npaths_mate*/0,
+ /*pathnum*/1,/*npaths*/1,/*artificial_mate_p*/false,/*npaths_mate*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*invertp*/false,
/*invert_mate_p*/false);
Pair_print_sam(fp,ABBREV_CONCORDANT_MULT,pairarray,npairs,/*cigar_tokens*/NULL,/*gmap_intronp*/false,
@@ -4044,7 +4053,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
@@ -4056,7 +4065,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
@@ -4069,13 +4078,15 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
SAM_print_nomapping(fp,ABBREV_PAIRED_MULT_XS,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_PAIRED_MULT_XS,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,/*npaths_mate*/npaths,
+ /*first_read_p*/false,/*pathnum*/1,npaths,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -4104,7 +4115,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
@@ -4116,7 +4127,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
}
@@ -4150,7 +4161,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/1,quality_shift,sam_read_group_id,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/1,quality_shift,sam_read_group_id,
invert_first_p,invert_second_p,merge_samechr_p);
/* Note: Do not act on add_paired_nomappers_p, since the two reads are artificially paired up already */
@@ -4163,7 +4174,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/1,quality_shift,sam_read_group_id,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/1,quality_shift,sam_read_group_id,
invert_second_p,invert_first_p,merge_samechr_p);
} else if (resulttype == UNPAIRED_MULT || resulttype == UNPAIRED_TRANSLOC) {
@@ -4222,8 +4233,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
stage3 = stage3array2[pathnum-1];
SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/stage3array1[pathnum-1],acc1,acc2,pathnum,npaths_max,
@@ -4232,8 +4243,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
/* Print remaining results with non-mappers */
@@ -4251,13 +4262,13 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
/* matching nomapper for second end */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,pathnum,/*npaths*/npaths_max,/*npaths_mate*/npaths_max,
- /*mate_chrpos*/chrpos5,
+ resulttype,/*first_read_p*/false,pathnum,npaths_max,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
@@ -4271,8 +4282,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* matching nomapper for first end */
SAM_print_nomapping(fp,abbrev,queryseq1,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/true,pathnum,/*npaths*/npaths_max,/*npaths_mate*/npaths_max,
- /*mate_chrpos*/chrpos3,
+ resulttype,/*first_read_p*/true,pathnum,npaths_max,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/NULL,acc1,acc2,pathnum,npaths_max,
@@ -4281,8 +4292,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
}
@@ -4311,14 +4322,14 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths2,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
} else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
/* Just printing one end as nomapping */
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/true,/*pathnum*/1,npaths1,/*npaths_mate*/npaths2,
- /*mate_chrpos*/chrpos3,
+ resulttype,/*first_read_p*/true,/*pathnum*/1,npaths1,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
} else {
@@ -4334,8 +4345,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths2,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
@@ -4365,14 +4376,14 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths1,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
} else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
/* Just printing one end as nomapping */
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,/*pathnum*/1,npaths2,/*npaths_mate*/npaths1,
- /*mate_chrpos*/chrpos5,
+ resulttype,/*first_read_p*/false,/*pathnum*/1,npaths2,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
} else {
@@ -4388,8 +4399,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths1,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
}
}
@@ -4471,8 +4482,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,npaths1,/*npaths_mate*/npaths2,
- /*mate_chrpos*/chrpos3,
+ /*first_read_p*/true,/*pathnum*/0,npaths1,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
@@ -4493,10 +4504,11 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,/*pathnum*/1,/*npaths*/npaths_max,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
+ resulttype,/*first_read_p*/false,/*pathnum*/1,npaths1,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
} else {
SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1,
@@ -4505,8 +4517,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths2,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
} else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
@@ -4516,8 +4528,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths1,/*npaths_mate*/npaths2,
- /*mate_chrpos*/chrpos3,
+ /*first_read_p*/true,/*pathnum*/1,npaths1,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
@@ -4534,7 +4546,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
npaths_max = npaths1; /* since npaths2 == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/false,pathnum,
- /*npaths*/npaths_max,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
+ npaths1,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths_max,
Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
@@ -4542,7 +4554,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
invert_first_p,invert_second_p,merge_samechr_p);
} else {
@@ -4552,8 +4564,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*npaths_mate*/npaths2,quality_shift,sam_read_group_id,
- invert_first_p,invert_second_p,merge_samechr_p);
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
}
@@ -4579,8 +4591,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/0,npaths2,/*npaths_mate*/npaths1,
- /*mate_chrpos*/chrpos5,
+ /*first_read_p*/false,/*pathnum*/0,npaths2,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
}
@@ -4597,7 +4609,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
npaths_max = npaths2; /* since npaths1 == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/true,/*pathnum*/1,
- /*npaths*/npaths_max,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
+ npaths2,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths_max,
Stage3end_absmq_score(stage3),first_absmq2,/*second_absmq2*/0,
@@ -4605,8 +4617,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
} else {
SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2,
@@ -4615,8 +4627,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths1,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
} else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
@@ -4626,8 +4638,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths2,/*npaths_mate*/npaths1,
- /*mate_chrpos*/chrpos5,
+ /*first_read_p*/false,/*pathnum*/1,npaths2,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
}
@@ -4644,7 +4656,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
npaths_max = npaths2; /* since npaths1 == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/true,pathnum,
- /*npaths*/npaths_max,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
+ npaths2,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths_max,
Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
@@ -4652,8 +4664,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
} else {
SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2,
@@ -4662,8 +4674,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
/*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*npaths_mate*/npaths1,quality_shift,sam_read_group_id,
- invert_second_p,invert_first_p,merge_samechr_p);
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
}
}
diff --git a/src/samprint.h b/src/samprint.h
index 9723497..4170329 100644
--- a/src/samprint.h
+++ b/src/samprint.h
@@ -1,4 +1,4 @@
-/* $Id: samprint.h 181904 2016-01-07 20:31:34Z twu $ */
+/* $Id: samprint.h 183725 2016-02-04 00:40:15Z twu $ */
#ifndef SAMPRINT_INCLUDED
#define SAMPRINT_INCLUDED
@@ -35,14 +35,14 @@ SAM_compute_chrpos (int hardclip_low, int hardclip_high, Stage3end_T this, int q
extern unsigned int
SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
- bool first_read_p, int pathnum, int npaths, int npaths_mate,
+ bool first_read_p, int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
int absmq_score, int first_absmq, bool invertp, bool invert_mate_p);
extern void
SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3end_T mate, char *acc1, char *acc2,
Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p,
- int pathnum, int npaths, int npaths_mate, Chrpos_T mate_chrpos,
- int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p);
+ int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
+ Chrpos_T mate_chrpos, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p);
extern void
SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
@@ -50,7 +50,7 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
Shortread_T queryseq2, int pairedlength, Chrpos_T chrpos, Chrpos_T mate_chrpos,
int clipdir, int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
- Resulttype_T resulttype, bool first_read_p, int npaths_mate, int quality_shift,
+ Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate, int quality_shift,
char *sam_read_group_id, bool invertp, bool invert_mate_p, bool merge_samechr_p);
extern void
diff --git a/src/stage2.c b/src/stage2.c
index acbc11c..c0e0e63 100644
--- a/src/stage2.c
+++ b/src/stage2.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage2.c 166741 2015-06-02 01:24:48Z twu $";
+static char rcsid[] = "$Id: stage2.c 183727 2016-02-04 00:40:29Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -2163,7 +2163,7 @@ score_querypos_lookforward_mult (
}
}
- while (hiti < nhits) {
+ while (hiti >= 0) {
/* Adjacent position not found for hiti */
currlink = &(links[querypos][hiti + low_hit]);
--
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