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Swarm 2.1.9: Fix compilation errors with GCC 6
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@torognes
torognes committed Jul 6, 2016
1 parent a84e112 commit 6aa9991
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Showing 5 changed files with 41 additions and 38 deletions.
5 changes: 4 additions & 1 deletion man/swarm.1
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@@ -1,5 +1,5 @@
.\" ============================================================================
.TH swarm 1 "March 11, 2016" "version 2.1.8" "USER COMMANDS"
.TH swarm 1 "July 6, 2016" "version 2.1.9" "USER COMMANDS"
.\" ============================================================================
.SH NAME
swarm \(em find clusters of nearly-identical nucleotide amplicons
Expand Down Expand Up @@ -329,6 +329,9 @@ New features and important modifications of \fBswarm\fR (short lived
or minor bug releases are not mentioned):
.RS
.TP
.BR v2.1.9\~ "released July 6, 2016"
Version 2.1.9 fixes errors when compiling with GCC version 6.
.TP
.BR v2.1.8\~ "released March 11, 2016"
Version 2.1.8 fixes a rare bug triggered when clustering extremely
short undereplicated sequences. Also, alignment parameters are not
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Binary file modified man/swarm_manual.pdf
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36 changes: 18 additions & 18 deletions src/search16.cc
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Expand Up @@ -155,31 +155,31 @@ inline void dprofile_fill16(WORD * dprofile_word,
" xorq %%r11, %%r11 \n"

#define ONESTEP(H, N, F, V, DIR) \
" paddusw "V", "H" \n" \
" movdqa "H", %%xmm13 \n" \
" pcmpgtw "F", %%xmm13 \n" \
" paddusw " V ", " H " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtw " F ", %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 0+"DIR" \n" \
" pminsw "F", "H" \n" \
" pminsw %%xmm12, "H" \n" \
" movdqa "H", %%xmm13 \n" \
" movw %%dx, 0+" DIR " \n" \
" pminsw " F ", " H " \n" \
" pminsw %%xmm12, " H " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpeqw %%xmm12, %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 2+"DIR" \n" \
" movdqa "H", "N" \n" \
" paddusw %%xmm14, "H" \n" \
" paddusw %%xmm15, "F" \n" \
" movw %%dx, 2+" DIR " \n" \
" movdqa " H ", " N " \n" \
" paddusw %%xmm14, " H " \n" \
" paddusw %%xmm15, " F " \n" \
" paddusw %%xmm15, %%xmm12 \n" \
" movdqa "H", %%xmm13 \n" \
" pcmpgtw "F", %%xmm13 \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtw " F ", %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 4+"DIR" \n" \
" movdqa "H", %%xmm13 \n" \
" movw %%dx, 4+" DIR " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtw %%xmm12, %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 6+"DIR" \n" \
" pminsw "H", %%xmm12 \n" \
" pminsw "H", "F" \n"
" movw %%dx, 6+" DIR " \n" \
" pminsw " H ", %%xmm12 \n" \
" pminsw " H ", " F " \n"


inline void donormal16(__m128i * Sm,
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36 changes: 18 additions & 18 deletions src/search8.cc
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Expand Up @@ -443,31 +443,31 @@ inline void dprofile_fill8(BYTE * dprofile,


#define ONESTEP(H, N, F, V, DIR) \
" paddusb "V", "H" \n" \
" movdqa "H", %%xmm13 \n" \
" pcmpgtb "F", %%xmm13 \n" \
" paddusb " V ", " H " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtb " F ", %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 0+"DIR" \n" \
" pminub "F", "H" \n" \
" pminub %%xmm12, "H" \n" \
" movdqa "H", %%xmm13 \n" \
" movw %%dx, 0+" DIR " \n" \
" pminub " F ", " H " \n" \
" pminub %%xmm12, " H " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpeqb %%xmm12, %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 2+"DIR" \n" \
" movdqa "H", "N" \n" \
" paddusb %%xmm14, "H" \n" \
" paddusb %%xmm15, "F" \n" \
" movw %%dx, 2+" DIR " \n" \
" movdqa " H ", " N " \n" \
" paddusb %%xmm14, " H " \n" \
" paddusb %%xmm15, " F " \n" \
" paddusb %%xmm15, %%xmm12 \n" \
" movdqa "H", %%xmm13 \n" \
" pcmpgtb "F", %%xmm13 \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtb " F ", %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 4+"DIR" \n" \
" movdqa "H", %%xmm13 \n" \
" movw %%dx, 4+" DIR " \n" \
" movdqa " H ", %%xmm13 \n" \
" pcmpgtb %%xmm12, %%xmm13 \n" \
" pmovmskb %%xmm13, %%edx \n" \
" movw %%dx, 6+"DIR" \n" \
" pminub "H", %%xmm12 \n" \
" pminub "H", "F" \n"
" movw %%dx, 6+" DIR " \n" \
" pminub " H ", %%xmm12 \n" \
" pminub " H ", " F " \n"

inline void donormal8(__m128i * Sm,
__m128i * hep,
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2 changes: 1 addition & 1 deletion src/swarm.h
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Expand Up @@ -52,7 +52,7 @@
#define LINE_MAX 2048
#endif

#define SWARM_VERSION "2.1.8"
#define SWARM_VERSION "2.1.9"
#define WIDTH 32
#define WIDTH_SHIFT 5
#define BLOCKWIDTH 32
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