[med-svn] [Git][med-team/grabix][upstream] New upstream version 0.1.7

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / grabix


Commits:
bb2e5a92 by Andreas Tille at 2018-10-28T13:14:46Z
New upstream version 0.1.7
- - - - -


4 changed files:

- grabix.cpp
- grabix.h
- test.sh
- − tests/empty.fastq.gz


Changes:

=====================================
grabix.cpp
=====================================
@@ -86,7 +86,7 @@ int create_grabix_index(string bgzf_file)
     int64_t offset = 0;
     while ((status = bgzf_getline(bgzf_fp, '\n', line)) >= 0)
     {
-        offset = bgzf_tell(bgzf_fp);
+        offset = bgzf_tell (bgzf_fp);
         if (line->s[0] != '#')
             break;
         prev_offset = offset;
@@ -104,10 +104,10 @@ int create_grabix_index(string bgzf_file)
     {
         // grab the next line and store the offset
         eof = bgzf_getline(bgzf_fp, '\n', line);
-        offset = bgzf_tell(bgzf_fp);
+        offset = bgzf_tell (bgzf_fp);
         chunk_count++;
         // stop if we have encountered an empty line
-        if (eof < 0 || offset == prev_offset)
+        if (eof <= 0)
         {
             if (bgzf_check_EOF(bgzf_fp) == 1) {
                 if (offset > prev_offset) {
@@ -116,7 +116,7 @@ int create_grabix_index(string bgzf_file)
                 }
                 break;
             }
-            break;
+            //break;
         }
         // store the offset of this chunk start
         else if (chunk_count == CHUNK_SIZE)
@@ -214,7 +214,7 @@ int grab(string bgzf_file, int64_t from_line, int64_t to_line)
         line->l = 0;
         line->m = 0;
 
-        while ((status = bgzf_getline(bgzf_fp, '\n', line)) > 0)
+        while ((status = bgzf_getline(bgzf_fp, '\n', line)) != 0)
         {
             if (line->s[0] == '#')
                 printf("%s\n", line->s);


=====================================
grabix.h
=====================================
@@ -7,7 +7,7 @@ using namespace std;
 #include "bgzf.h"
 
 
-#define VERSION "0.1.8"
+#define VERSION "0.1.7"
 // we only want to store the offset for every 10000th
 // line. otherwise, were we to store the position of every
 // line in the file, the index could become very large for


=====================================
test.sh
=====================================
@@ -9,29 +9,13 @@ echo "indexing"
 time ./grabix index $FQ
 echo "indexed"
 python tests/test-fastq.py $FQ
-a=$(./grabix grab test.cnt.gz $(($lines * 4)))
+a=$(grabix grab test.cnt.gz $(($lines * 4)))
 b=$(zless $FQ | tail -1)
 if [[ "$a" != "$b" ]]; then
 	echo FAIL last record
-    exit 1
-else
-	echo OK last record
 fi
 rm -f ${FQ}{,.gbi}
 
-rm -f tests/empty.fastq.gz.gbi
-./grabix index tests/empty.fastq.gz
-
-a=$(cat tests/empty.fastq.gz.gbi | awk 'NR == 2')
-if [[ "$a" != "16" ]]; then
-    echo FAIL index wrong size
-    exit 1
-else
-    echo "OK index size"
-fi
-
-
-
 for V in  \
 	test.PLs.vcf \
 	test.auto_dom.no_parents.2.vcf \


=====================================
tests/empty.fastq.gz deleted
=====================================
Binary files a/tests/empty.fastq.gz and /dev/null differ



View it on GitLab: https://salsa.debian.org/med-team/grabix/commit/bb2e5a92f2d5ce1e285e7dbcef1788384a7c52d2

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View it on GitLab: https://salsa.debian.org/med-team/grabix/commit/bb2e5a92f2d5ce1e285e7dbcef1788384a7c52d2
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