Merge branch 'develop'

.travis.yml

@@ -96,8 +96,6 @@ before_install:
   - if [[ -n "${MY_CXX}" ]]; then export CXX="${MY_CXX}"; fi
   - if [[ -n "${MY_CFLAGS}" ]]; then export CFLAGS="${MY_CFLAGS}"; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then rvm get stable || true; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update || true; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install cmake || brew upgrade cmake || true; fi
 
 install:
   - if [[ "$BUILD_TYPE" == "docker" ]]; then docker pull $DOCKER_IMAGE; fi

CHANGELOG.md

@@ -7,6 +7,18 @@ This project follows the [Gitflow Workflow model](https://www.atlassian.com/git/
 ## [Unreleased]
 The Unreleased section will be empty for tagged releases. Unreleased functionality appears in the develop branch.
 
+## [2.4.3] - 2020-11-23
+### Fixed
+- provide action-if-not-found case for PKG_CHECK_MODULES([Z])
+  Thanks to [ksahlin] for the bug report.
+- spellcheck parasail_aligner, thanks to [nileshpatra].
+
+### Closed Issues
+- Failed to build parasail on Mac OSx [\#81]
+
+### Merged Pull Requests
+- Fix spellings [\#78]
+
 ## [2.4.2] - 2020-04-15
 ### Fixed
 - Add missing headers to make dist target, use distcheck in Travis.
@@ -386,7 +398,8 @@ The Unreleased section will be empty for tagged releases. Unreleased functionali
 ## [1.0.0] - 2015-09-16
 First stable, production-ready version of parasail.
 
-[Unreleased]: https://github.com/jeffdaily/parasail/compare/v2.4.2...develop
+[Unreleased]: https://github.com/jeffdaily/parasail/compare/v2.4.3...develop
+[2.4.3]: https://github.com/jeffdaily/parasail/compare/v2.4.2...v2.4.3
 [2.4.2]: https://github.com/jeffdaily/parasail/compare/v2.4.1...v2.4.2
 [2.4.1]: https://github.com/jeffdaily/parasail/compare/v2.4...v2.4.1
 [2.4]:   https://github.com/jeffdaily/parasail/compare/v2.3...v2.4
@@ -416,6 +429,10 @@ First stable, production-ready version of parasail.
 [1.0.1]: https://github.com/jeffdaily/parasail/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/jeffdaily/parasail/releases/tag/v1.0.0
 
+[\#81]: https://github.com/jeffdaily/parasail/issues/81
+[\#80]: https://github.com/jeffdaily/parasail/issues/80
+[\#79]: https://github.com/jeffdaily/parasail/issues/79
+[\#78]: https://github.com/jeffdaily/parasail/pull/78
 [\#77]: https://github.com/jeffdaily/parasail/pull/77
 [\#76]: https://github.com/jeffdaily/parasail/issues/76
 [\#75]: https://github.com/jeffdaily/parasail/issues/75
@@ -506,3 +523,5 @@ First stable, production-ready version of parasail.
 [GrappoloTK]: https://github.com/luhowardmark/GrappoloTK
 [SSW]: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
 [kseq.h]: http://lh3lh3.users.sourceforge.net/kseq.shtml
+[nileshpatra]: https://github.com/nileshpatra
+[ksahlin]: https://github.com/ksahlin

apps/README.md

@@ -33,7 +33,7 @@ Defaults:
             file: no default, must be in FASTA format
       query_file: no default, must be in FASTA format
      output_file: parasail.csv
-   output_format: no deafult, must be one of {EMBOSS,SAM,SAMH,SSW}
+   output_format: no default, must be one of {EMBOSS,SAM,SAMH,SSW}
       batch_size: 0 (calculate based on memory budget),
                   how many alignments before writing output
    memory_budget: 2GB or half available from system query (135.185 GB)

apps/parasail_aligner.cpp

@@ -342,7 +342,7 @@ THREAD_DOC
             "            file: no default, must be in FASTA format\n"
             "      query_file: no default, must be in FASTA format\n"
             "     output_file: parasail.csv\n"
-            "   output_format: no deafult, must be one of {EMBOSS,SAM,SAMH,SSW}\n"
+            "   output_format: no default, must be one of {EMBOSS,SAM,SAMH,SSW}\n"
             "      batch_size: 0 (calculate based on memory budget),\n"
             "                  how many alignments before writing output\n"
             "   memory_budget: 2GB or half available from system query (%.3f GB)\n"
@@ -1331,24 +1331,24 @@ int main(int argc, char **argv) {
             eprintf(stdout, "%20s: %.4f seconds\n", "clamp LCP time", finish-start);
         }
 
-        /* The GSA we create will put all sentinals either at the beginning
+        /* The GSA we create will put all sentinels either at the beginning
          * or end of the SA. We don't want to count all of the terminals,
          * nor do we want to process them in our bottom-up traversal. */
-        /* do the sentinals appear at the beginning or end of SA? */
+        /* do the sentinels appear at the beginning or end of SA? */
         int bup_start = 1;
         int bup_stop = n;
         if (T[SA[0]] == sentinal) {
-            /* sentinals at beginning */
+            /* sentinels at beginning */
             bup_start = sid+1;
             bup_stop = n;
         }
         else if (T[SA[n-1]] == sentinal) {
-            /* sentinals at end */
+            /* sentinels at end */
             bup_start = 1;
             bup_stop = n-sid;
         }
         else {
-            eprintf(stderr, "sentinals not found at beginning or end of SA\n");
+            eprintf(stderr, "sentinels not found at beginning or end of SA\n");
             exit(EXIT_FAILURE);
         }
 
@@ -1484,7 +1484,7 @@ int main(int argc, char **argv) {
     if (vpairs.empty()) {
         if (pairs.empty()) {
             if (use_filter) {
-                eprintf(stderr, "no alignment work, either the filter removed all alignemnts or the input file(s) were empty\n");
+                eprintf(stderr, "no alignment work, either the filter removed all alignments or the input file(s) were empty\n");
                 exit(EXIT_FAILURE);
             }
             else {

configure.ac

@@ -54,6 +54,7 @@ AC_SUBST([PACKAGE_VERSION])
 # parasail version 2.4.0: 7:0:4 (ABI version 7) added functions
 # parasail version 2.4.1: 7:1:4 (ABI version 7)
 # parasail version 2.4.2: 7:2:4 (ABI version 7)
+# parasail version 2.4.3: 7:2:4 (ABI version 7) no change
 #
 # libparasail -version-info current:revision:age
 LTVER="7:2:4"
@@ -1096,7 +1097,7 @@ AC_ARG_WITH([zlib],
 zlib_okay_val=0
 AS_IF([test "x$with_zlib" = xno], [], [
 m4_ifdef([PKG_CHECK_MODULES],
-         [PKG_CHECK_MODULES([Z], [zlib], [zlib_okay_val=1])],
+         [PKG_CHECK_MODULES([Z], [zlib], [zlib_okay_val=1], [zlib_okay_val=0])],
          [
 parasail_save_LIBS="$LIBS"
 AC_CHECK_HEADERS([zlib.h])

parasail.h

@@ -18,7 +18,7 @@ extern "C" {
 /* Version macros for compile-time API version detection */
 #define PARASAIL_VERSION_MAJOR 2
 #define PARASAIL_VERSION_MINOR 4
-#define PARASAIL_VERSION_PATCH 2
+#define PARASAIL_VERSION_PATCH 3
 
 #define PARASAIL_MAKE_VERSION(major, minor, patch) \
     ((major) * 10000 + (minor) * 100 + (patch))

tests/test_openmp_sais.cpp

@@ -12,7 +12,7 @@
  * For each sequence pair, performs semi-global alignment.
  *
  * Note about the input file. It is expected to be a packed fasta file
- * with each sequence delimited by the '$' sentinal. For example,
+ * with each sequence delimited by the '$' sentinel. For example,
  * "banana$mississippi$foo$bar$".
  */
 #include "config.h"
@@ -256,7 +256,7 @@ int main(int argc, char **argv) {
 
     T[n]='\0'; /* so we can print it */
 
-    /* determine sentinal */
+    /* determine sentinel */
     if (sentinal == 0) {
         int off = 0;
         while (!isgraph(T[n-off])) {
@@ -290,8 +290,8 @@ int main(int argc, char **argv) {
     }
     longest += 1;
     assert(BEG.size()==END.size()+1);
-    if (0 == sid) { /* no sentinal found */
-        fprintf(stdout, "no sentinal(%c) found in input\n", sentinal);
+    if (0 == sid) { /* no sentinel found */
+        fprintf(stdout, "no sentinel(%c) found in input\n", sentinal);
         exit(EXIT_FAILURE);
     }
 
@@ -317,30 +317,30 @@ int main(int argc, char **argv) {
     /* "fix" the LCP array to clamp LCP's that are too long */
     start = timer_real();
     for (i = 0; i < n; ++i) {
-        int len = END[SID[SA[i]]] - SA[i]; /* don't include sentinal */
+        int len = END[SID[SA[i]]] - SA[i]; /* don't include sentinel */
         if (LCP[i] > len) LCP[i] = len;
     }
     finish = timer_real();
     fprintf(stdout, " clamp LCP: %.4f sec\n", finish-start);
 
-    /* The GSA we create will put all sentinals either at the beginning
+    /* The GSA we create will put all sentinels either at the beginning
      * or end of the SA. We don't want to count all of the terminals,
      * nor do we want to process them in our bottom-up traversal. */
-    /* do the sentinals appear at the beginning or end of SA? */
+    /* do the sentinels appear at the beginning or end of SA? */
     int bup_start = 1;
     int bup_stop = n;
     if (T[SA[0]] == sentinal) {
-        /* sentinals at beginning */
+        /* sentinels at beginning */
         bup_start = sid+1;
         bup_stop = n;
     }
     else if (T[SA[n-1]] == sentinal) {
-        /* sentinals at end */
+        /* sentinels at end */
         bup_start = 1;
         bup_stop = n-sid;
     }
     else {
-        fprintf(stdout, "sentinals not found at beginning or end of SA\n");
+        fprintf(stdout, "sentinels not found at beginning or end of SA\n");
     }
 
     /* DFS of enhanced SA, from Abouelhoda et al */