diff --git a/.travis.yml b/.travis.yml index ccff3f6c..00e98c95 100644 --- a/.travis.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index a8f0163f..05513a70 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/apps/README.md b/apps/README.md index 458c5d91..6fb775cf 100644 --- a/apps/README.md +++ b/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) diff --git a/apps/parasail_aligner.cpp b/apps/parasail_aligner.cpp index fe95bca9..ca810495 100644 --- a/apps/parasail_aligner.cpp +++ b/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 { diff --git a/configure.ac b/configure.ac index 527c2b74..c19fb213 100644 --- a/configure.ac +++ b/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="$LIBS" AC_CHECK_HEADERS([zlib.h]) diff --git a/parasail.h b/parasail.h index b4ae49de..ec397caf 100644 --- a/parasail.h +++ b/parasail.h @@ -18,7 +18,7 @@ extern "C" { /* Version macros for compile-time API version detection */ #define PARASAIL_VERSION_MAJOR 2 #define PARASAIL_VERSION_MINOR 4 -#define PARASAIL_VERSION_PATCH 2 +#define PARASAIL_VERSION_PATCH 3 #define PARASAIL_MAKE_VERSION(major, minor, patch) \ ((major) * 10000 + (minor) * 100 + (patch)) diff --git a/tests/test_openmp_sais.cpp b/tests/test_openmp_sais.cpp index 93e98dfb..94f66eb5 100644 --- a/tests/test_openmp_sais.cpp +++ b/tests/test_openmp_sais.cpp @@ -12,7 +12,7 @@ * For each sequence pair, performs semi-global alignment. * * Note about the input file. It is expected to be a packed fasta file - * with each sequence delimited by the '$' 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 */