bump version to 2.3, update CHANGELOG.md and README.md

CHANGELOG.md

@@ -7,6 +7,12 @@ 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.
 
+## [2.3] - 2018-10-23
+### Added
+- Support for MSYS and mingw builds.
+- parasail_aligner outputs version information in verbose mode.
+- Functions `parasail_result_get_traceback` and `parasail_traceback_free` to retrieve traceback C strings. See [README.md] for details.
+
 ## [2.2] - 2018-07-10
 ### Added
 - ARM NEON vectorized functions via the [simde] project. Also thanks to [philres] for the hardware donation. 
@@ -324,7 +330,8 @@ 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/v2.2...develop
+[Unreleased]: https://github.com/jeffdaily/parasail/compare/v2.3...develop
+[2.3]:   https://github.com/jeffdaily/parasail/compare/v2.2...v2.3
 [2.2]:   https://github.com/jeffdaily/parasail/compare/v2.1.5...v2.2
 [2.1.5]: https://github.com/jeffdaily/parasail/compare/v2.1.4...v2.1.5
 [2.1.4]: https://github.com/jeffdaily/parasail/compare/v2.1.3...v2.1.4
@@ -350,6 +357,10 @@ 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
 
+[\#63]: https://github.com/jeffdaily/parasail/issues/63
+[\#62]: https://github.com/jeffdaily/parasail/issues/62
+[\#61]: https://github.com/jeffdaily/parasail/issues/61
+[\#60]: https://github.com/jeffdaily/parasail/issues/60
 [\#59]: https://github.com/jeffdaily/parasail/issues/59
 [\#58]: https://github.com/jeffdaily/parasail/issues/58
 [\#57]: https://github.com/jeffdaily/parasail/issues/57
@@ -410,6 +421,7 @@ First stable, production-ready version of parasail.
 [\#2]: https://github.com/jeffdaily/parasail/issues/2
 [\#1]: https://github.com/jeffdaily/parasail/issues/1
 
+[README.md]: README.md
 [philres]: https://github.com/philres
 [simde]: https://github.com/nemequ/simde
 [manylinux]: https://github.com/pypa/manylinux

README.md

@@ -483,7 +483,7 @@ void parasail_sequences_free(parasail_sequences_t *sequences);
 
 [back to top]
 
-Parasail supports both printing a traceback to stdout as well as accessing a SAM CIGAR string from a result.  You must use a traceback-capable alignment function.  Refer to the C interface description above for details on how to use a traceback-capable alignment function.
+Parasail supports printing a traceback to stdout, accessing a SAM CIGAR string from a result, as well as returning the three alignment strings.  You must use a traceback-capable alignment function.  Refer to the C interface description above for details on how to use a traceback-capable alignment function.
 
 #### Printing Tracebacks
 
@@ -503,6 +503,22 @@ void parasail_traceback_generic(
         int width,  /* width of traceback to display before wrapping */
         int name_width,
         int use_stats); /* if 0, don't display stats, if non-zero, summary stats displayed */
+
+void parasail_traceback_generic_extra(
+        const char *seqA, int lena,
+        const char *seqB, int lenb,
+        const char *nameA,
+        const char *nameB,
+        const parasail_matrix_t *matrix,
+        parasail_result_t *result,
+        char match, /* character to use for a match */
+        char pos,   /* character to use for a positive-value mismatch */
+        char neg,   /* character to use for a negative-value mismatch */
+        int width,  /* width of traceback to display before wrapping */
+        int name_width,
+        int use_stats, /* if 0, don't display stats, if non-zero, summary stats displayed */
+        int int_width, /* width used for reference and query indexes */
+        FILE *stream); /* to print to custom file stream */
 ```
 
 For example, `parasail_traceback_generic(seqA, strlen(seqA), seqB, strlen(seqB), "Query:", "Target:", matrix, result, '|', '*', '*', 60, 7, 1)` might produce the following:
@@ -554,6 +570,32 @@ uint32_t parasail_cigar_decode_len(uint32_t cigar_int);
 char* parasail_cigar_decode(parasail_cigar_t *cigar);
 ```
 
+#### Traceback strings
+
+[back to top]
+
+The traceback can be returned as a set of three strings, all of equal length, representing the traceback.  Indels in the `query` or `ref` strings are represented by a dash `-`.  The `comp` string represents the comparison between the `query` and `ref` strings and can use custom characters for the `match` (exact match), `pos` (positive-valued inexact match), and `neg` (negative-valued non-match).
+
+```C
+typedef struct parasail_traceback_{
+    char *query;
+    char *comp;
+    char *ref;
+} parasail_traceback_t;
+
+extern parasail_traceback_t* parasail_result_get_traceback(
+        parasail_result_t *result,
+        const char *seqA,
+        int lena,
+        const char *seqB,
+        int lenb,
+        const parasail_matrix_t *matrix,
+        char match, char pos, char neg);
+
+extern void parasail_traceback_free(parasail_traceback_t *traceback);
+
+```
+
 ## Language Bindings
 
 [back to top]

configure.ac

@@ -49,10 +49,11 @@ AC_SUBST([PACKAGE_VERSION])
 # parasail version 2.1.3: 4:1:1 (ABI version 4) no change
 # parasail version 2.1.4: 4:2:1 (ABI version 4)
 # parasail version 2.1.5: 4:2:1 (ABI version 4) no change
-# parasail version 2.2.0: 5:0:2 (ABI version 4) added functions
+# parasail version 2.2.0: 5:0:2 (ABI version 5) added functions
+# parasail version 2.3.0: 6:0:3 (ABI version 6) added functions
 #
 # libparasail -version-info current:revision:age
-LTVER="5:0:2"
+LTVER="6:0:3"
 AC_SUBST([LTVER])
 
 ###############################################################################

parasail.h

@@ -17,7 +17,7 @@ extern "C" {
 
 /* Version macros for compile-time API version detection */
 #define PARASAIL_VERSION_MAJOR 2
-#define PARASAIL_VERSION_MINOR 2
+#define PARASAIL_VERSION_MINOR 3
 #define PARASAIL_VERSION_PATCH 0
 
 #define PARASAIL_MAKE_VERSION(major, minor, patch) \