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Merge branch 'release-0.43'

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nawrockie committed Jul 2, 2016
2 parents 9d9ecea + d2040a3 commit bdfb76ae1cd7ae532e89b01c29f7bf2c61db37a7
Showing with 604 additions and 324 deletions.
  1. +5 −5 configure.ac
  2. +18 −2 esl_avx.c
  3. +8 −0 esl_dsqdata.c
  4. +0 −9 esl_dsqdata.h
  5. +7 −0 esl_gencode.c
  6. +24 −0 esl_msa_testfiles/afa/afa.good.3
  7. +9 −0 esl_msa_testfiles/phylip/phylip.ambig.1
  8. +90 −175 esl_msafile.c
  9. +2 −2 esl_msafile.h
  10. +181 −0 esl_msafile.md
  11. +7 −7 esl_msafile_a2m.c
  12. +5 −28 esl_msafile_afa.c
  13. +218 −85 esl_msafile_phylip.c
  14. +19 −7 esl_sqio_ascii.c
  15. +11 −4 esl_sqio_ncbi.c
@@ -45,7 +45,7 @@ AC_PREREQ(2.63)
################################################################
# 2. AC_INIT
################################################################
AC_INIT(Easel, 0.42, sean@eddylab.org, easel)
AC_INIT(Easel, 0.43, sean@eddylab.org, easel)
AC_MSG_NOTICE([Configuring the Easel library for your system.])

# remember if the user is overriding CFLAGS
@@ -62,13 +62,13 @@ fi
# The four AC_INIT args above set the following output variables and preprocessor
# symbols:
# PACKAGE_NAME <package> e.g. "Easel"
# PACKAGE_VERSION <version> e.g. "0.42"
# PACKAGE_VERSION <version> e.g. "0.43"
# PACKAGE_BUGREPORT <bug-report> e.g. "sean@eddylab.org"
# PACKAGE_TARNAME <tarname> e.g. "easel"
# From them, AC_INIT automatically derives one more:
# PACKAGE_STRING <package> <version>, e.g. "Easel 0.42"
# PACKAGE_STRING <package> <version>, e.g. "Easel 0.43"
# Then we define some of our own:
# EASEL_DATE release date: e.g. "May 2016"
# EASEL_DATE release date: e.g. "July 2016"
# EASEL_COPYRIGHT one-line copyright string
# EASEL_LICENSE one-line license string
# EASEL_LICENSETAG which license to bundle from Licenses/ subdirectory.
@@ -84,7 +84,7 @@ fi
# EASEL_VERSION e.g. "1.9a"
#

EASEL_DATE="May 2016"
EASEL_DATE="July 2016"
EASEL_COPYRIGHT="Copyright (C) 2016 Howard Hughes Medical Institute"
EASEL_LICENSE="Freely distributed under the BSD open source license."
EASEL_VERSION=$PACKAGE_VERSION
@@ -1,8 +1,24 @@
#include <stdio.h>
#ifdef HAVE_AVX2
// This file is just a dummy target to make sure that the functions defined in esl_avx.h get included in the library version of hmmer
#include <immintrin.h> /* AVX2 */
#endif
#include "esl_avx.h"

#else /* ! HAVE_AVX2 */

/* If we don't have AVX compiled in, provide some nothingness to:
* a. prevent Mac OS/X ranlib from bitching about .o file that "has no symbols"
* b. prevent compiler from bitching about "empty compilation unit"
* c. automatically pass the automated tests.
*/
#include "easel.h"

void esl_avx_DoAbsolutelyNothing(void) { return; }
#if defined eslAVX_TESTDRIVE || eslAVX_EXAMPLE || eslAVX_BENCHMARK
int main(void) { return 0; }
#endif

#endif /* HAVE_AVX or not*/



// This file is just a dummy target to make sure that the functions defined in esl_avx.h get included in the library version of hmmer
@@ -52,6 +52,14 @@ static int dsqdata_unpack2(uint32_t *psq, ESL_DSQ *dsq, int *ret_L, int *ret_P
static int dsqdata_pack5 (ESL_DSQ *dsq, int L, uint32_t *psq, int *ret_P);
static int dsqdata_pack2 (ESL_DSQ *dsq, int L, uint32_t *psq, int *ret_P);


/* Embedded magic numbers allow us to validate the correct binary
* format, with version (if needed in the future), and to detect
* byteswapping.
*/
static uint32_t eslDSQDATA_MAGIC_V1 = 0xc4d3d1b1; // "dsq1" + 0x80808080
static uint32_t eslDSQDATA_MAGIC_V1SWAP = 0xb1d1d3c4; // ... as above, but byteswapped.

/*****************************************************************
*# 1. <ESL_DSQDATA>: reading dsqdata format
*****************************************************************/
@@ -117,15 +117,6 @@ typedef struct esl_dsqdata_s {




/* Embedded magic numbers allow us to validate the correct binary
* format, with version (if needed in the future), and to detect
* byteswapping.
*/
static uint32_t eslDSQDATA_MAGIC_V1 = 0xc4d3d1b1; // "dsq1" + 0x80808080
static uint32_t eslDSQDATA_MAGIC_V1SWAP = 0xb1d1d3c4; // ... as above, but byteswapped.


/* Defaults for size of eslDSQDATA_CHUNK
*/
#define eslDSQDATA_CHUNK_MAXSEQ 4096 // max number of sequences
@@ -731,6 +731,13 @@ esl_gencode_WorkstateDestroy(ESL_GENCODE_WORKSTATE *wrk)
if (wrk)
{
for (f = 0; f < 3; f++) esl_sq_Destroy(wrk->psq[f]);

if(wrk->orf_block != NULL)
{
esl_sq_DestroyBlock(wrk->orf_block);
wrk->orf_block = NULL;
}

free(wrk);
}
}
@@ -0,0 +1,24 @@
>7295730___KOG0003
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrilaqkyncdkmicrkcy
arlhpratncrkkkcghtnnlrpkkklk
>Hs4507761___KOG0003
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrqlaqkyncdkmicrkcy
arlhpravncrkkkcghtnnlrpkkkvk
>At3g52590___KOG0003
mqifvktltgktitlevessdtidnvkakiqdkegippdqqrlifagkql
edgrtladyniqkestlhlvlrlrggiiepslmmlarkynqdkmicrkcy
arlhpravncrkkkcghsnqlrpkkkik
>CE15495___KOG0003
mqifvktltgktitleveasdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrqlaqkyncdkqicrkcy
arlpprasncrkkkcghsselrikkklk
>SPAC1805.12c___KOG0003
mqifvktltgktitlevessdtidnvkskiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslkalaskyncekqicrkcy
arlppratncrkkkcghtnqlrpkkklk
>YIL148w___KOG0003
mqifvktltgktitlevessdtidnvkskiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslkalaskyncdksvcrkcy
arlppratncrkrkcghtnqlrpkkklk
@@ -0,0 +1,9 @@
2 49
seq1 AAAAAAAAAA CCCCCCCCCC
YYYYYYYYY DDDDDDDDDD EEEEEEEEEE
YYYYYYYYY FFFFFFFFFF GGGGGGGGGG
HHHHHHHHH IIIIIIIIII KKKKKKKKKK




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