[med-svn] [fermi-lite] 02/02: kmer_correct added by jwala for libSeqLib

[Andreas Tille]

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tille pushed a commit to branch master
in repository fermi-lite.

commit 49c22fb7a8425c7425b34e9ab4704424e38e5541
Author: Andreas Tille <tille at debian.org>
Date:   Fri Feb 3 11:10:39 2017 +0100

    kmer_correct added by jwala for libSeqLib
---
 debian/patches/bcf_seqlib.patch | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

diff --git a/debian/patches/bcf_seqlib.patch b/debian/patches/bcf_seqlib.patch
index d4b2a5d..1035478 100644
--- a/debian/patches/bcf_seqlib.patch
+++ b/debian/patches/bcf_seqlib.patch
@@ -169,13 +169,11 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
  static uint64_t max_streak(int k, const bfc_ch_t *ch, const fml_seq1_t *s)
  {
  	int i, l;
-@@ -663,6 +543,21 @@ float fml_correct_core(const fml_opt_t *
+@@ -663,6 +543,18 @@ float fml_correct_core(const fml_opt_t *
  	return kcov;
  }
  
-+//jwala added here (linker issues)
-+// copied from fml_correct_core
-+/* Andreas Tille <tille at debian.org>: uncomment for the moment - would like to see what linker issues might actually happen
++// Added by jwala for use in libSeqLib
 +void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch) {
 +  int i = 0;
 +  es->e = (bfc_ec1buf_t**)calloc(es->opt->n_threads, sizeof(void*)); //jwala added cast
@@ -186,14 +184,13 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
 +    ec1buf_destroy(es->e[i]);
 +  free(es->e);
 +}
-+*/
 +
  float fml_correct(const fml_opt_t *opt, int n, fml_seq1_t *seq)
  {
  	return fml_correct_core(opt, 0, n, seq);
 --- /dev/null
 +++ b/bfc.h
-@@ -0,0 +1,163 @@
+@@ -0,0 +1,153 @@
 +#ifndef AC_BFC_H__
 +#define AC_BFC_H__
 +
@@ -343,17 +340,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100
 +	fml_seq1_t *seqs;
 +} ec_step_t;
 +
-+//void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch);
++void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch);
 +void bfc_opt_init(bfc_opt_t *opt);
 +
-+/*
-+ * FIXME: This leads to
-+/usr/include/fml/bfc.h: At global scope:
-+/usr/include/fml/bfc.h:153:22: warning: ‘bfc_ec1buf_t* ec1buf_init(const bfc_opt_t*, const bfc_ch_t*)’ used but never defined
-+ static bfc_ec1buf_t *ec1buf_init(const bfc_opt_t *opt, const bfc_ch_t *ch);
-+                      ^~~~~~~~~~~
-+ * warnings - but the declaration is needed in libSeqLib
-+ */
-+static bfc_ec1buf_t *ec1buf_init(const bfc_opt_t *opt, const bfc_ch_t *ch);
-+
 +#endif

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