[med-svn] [Git][med-team/gmap][upstream] New upstream version 2023-10-10+ds

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / gmap


Commits:
8a56fd82 by Étienne Mollier at 2023-10-14T20:19:35+02:00
New upstream version 2023-10-10+ds
- - - - -


3 changed files:

- ChangeLog
- VERSION
- src/shortread.c


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,6 @@
+2023-10-10 06:33:52 -0700 Printing hardclipped regions together with poly-A regions
+src/shortread.c
+
 2023-10-04 10:19:14 -0700 Updated version number
 VERSION
 config.site.rosalind.prd


=====================================
VERSION
=====================================
@@ -1 +1 @@
-2023-10-01
\ No newline at end of file
+2023-10-10
\ No newline at end of file


=====================================
src/shortread.c
=====================================
@@ -4986,27 +4986,24 @@ Shortread_print_hardclipped_reverse_quality (Filestring_T fp, T this, int hardcl
 /* For samprint XH field and print_fusion */
 void
 Shortread_print_chopped_end (Filestring_T fp, T this, int hardclip_low, int hardclip_high) {
-#ifdef PRINT_INDIVIDUAL_CHARS
-  int i;
-#endif
 
   if (hardclip_low > 0) {
-#ifdef PRINT_INDIVIDUAL_CHARS
-    for (i = 0; i < hardclip_low; i++) {
-      FPRINTF(fp,"%c",this->contents[i]);
+    if (this->left_choplength == 0) {
+      FPRINTF(fp,"%.*s",hardclip_low,&(this->contents[0]));
+    } else {
+      hardclip_low -= this->left_choplength;
+      FPRINTF(fp,"%s",this->left_chop);
+      FPRINTF(fp,"%.*s",hardclip_low,&(this->contents[0]));
     }
-#else
-    FPRINTF(fp,"%.*s",hardclip_low,&(this->contents[0]));
-#endif
     
   } else {
-#ifdef PRINT_INDIVIDUAL_CHARS
-    for (i = this->fulllength - hardclip_high; i < this->fulllength; i++) {
-      FPRINTF(fp,"%c",this->contents[i]);
+    if (this->right_choplength == 0) {
+      FPRINTF(fp,"%.*s",hardclip_high,&(this->contents[this->fulllength - hardclip_high]));
+    } else {
+      hardclip_high -= this->right_choplength;
+      FPRINTF(fp,"%.*s",hardclip_high,&(this->contents[this->fulllength - hardclip_high]));
+      FPRINTF(fp,"%s",this->right_chop);
     }
-#else
-    FPRINTF(fp,"%.*s",hardclip_high,&(this->contents[this->fulllength - hardclip_high]));
-#endif
   }
 
   return;
@@ -5017,22 +5014,21 @@ void
 Shortread_print_chopped_end_revcomp (Filestring_T fp, T this, int hardclip_low, int hardclip_high) {
 
   if (hardclip_low > 0) {
-#ifdef PRINT_INDIVIDUAL_CHARS
-    for (i = this->fulllength - 1; i >= this->fulllength - hardclip_low; --i) {
-      FPRINTF(fp,"%c",complCode[(int) this->contents[i]]);
+    if (this->right_choplength == 0) {
+      FPRINTF(fp,"%.*R",hardclip_low,&(this->contents[this->fulllength - hardclip_low]));
+    } else {
+      hardclip_low -= this->right_choplength;
+      FPRINTF(fp,"%.*R",this->right_choplength,this->right_chop);
+      FPRINTF(fp,"%.*R",hardclip_low,&(this->contents[this->fulllength - hardclip_low]));
     }
-#else
-    FPRINTF(fp,"%.*R",hardclip_low,&(this->contents[this->fulllength - hardclip_low]));
-#endif
-
   } else {
-#ifdef PRINT_INDIVIDUAL_CHARS
-    for (i = hardclip_high - 1; i >= 0; --i) {
-      FPRINTF(fp,"%c",complCode[(int) this->contents[i]]);
+    if (this->left_choplength == 0) {
+      FPRINTF(fp,"%.*R",hardclip_high,&(this->contents[0]));
+    } else {
+      hardclip_high -= this->left_choplength;
+      FPRINTF(fp,"%.*R",hardclip_high,&(this->contents[0]));
+      FPRINTF(fp,"%.*R",this->left_choplength,this->left_chop);
     }
-#else
-    FPRINTF(fp,"%.*R",hardclip_high,&(this->contents[0]));
-#endif
   }
 
   return;



View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/8a56fd827fcc796c728f268bfe85a354270ea68f

-- 
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/8a56fd827fcc796c728f268bfe85a354270ea68f
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