[med-svn] [Git][med-team/gmap][master] 4 commits: routine-update: New upstream version

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / gmap


Commits:
ff1ec4a0 by Étienne Mollier at 2023-10-14T20:19:34+02:00
routine-update: New upstream version

- - - - -
8a56fd82 by Étienne Mollier at 2023-10-14T20:19:35+02:00
New upstream version 2023-10-10+ds
- - - - -
ca685ca6 by Étienne Mollier at 2023-10-14T20:19:42+02:00
Update upstream source from tag 'upstream/2023-10-10+ds'

Update to upstream version '2023-10-10+ds'
with Debian dir 24876b882fe76bcdd5cd45081decdf25a0dad512
- - - - -
c6eaf77c by Étienne Mollier at 2023-10-14T20:32:59+02:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- ChangeLog
- VERSION
- debian/changelog
- 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


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+gmap (2023-10-10+ds-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 14 Oct 2023 20:21:01 +0200
+
 gmap (2023-10-01+ds-1) unstable; urgency=medium
 
   * Team upload.


=====================================
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/-/compare/e6bc235d50cd0f7f4553dc532126242ca6d446fb...c6eaf77c456a4e1776278ea6fa698d0eaeae30f9

-- 
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/compare/e6bc235d50cd0f7f4553dc532126242ca6d446fb...c6eaf77c456a4e1776278ea6fa698d0eaeae30f9
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