101 lines
3.3 KiB
Diff
101 lines
3.3 KiB
Diff
Amend command-line names for Gentoo SLOTed hmmer:2
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--- a/src/ehmmalign.c
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+++ b/src/ehmmalign.c
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@@ -99,7 +99,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign"));
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+ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2"));
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if(mapali)
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ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali));
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if(withali)
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--- a/src/ehmmbuild.c
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+++ b/src/ehmmbuild.c
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@@ -146,7 +146,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2"));
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if(prior)
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ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior));
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if(null)
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--- a/src/ehmmcalibrate.c
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+++ b/src/ehmmcalibrate.c
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@@ -98,7 +98,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2"));
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if(cpu)
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ajFmtPrintAppS(&cmd, " --cpu %d ", cpu);
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if(fixed)
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--- a/src/ehmmconvert.c
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+++ b/src/ehmmconvert.c
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@@ -72,7 +72,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2"));
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/* ACD option only allows one selection */
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option = ajStrGetCharFirst(format);
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--- a/src/ehmmemit.c
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+++ b/src/ehmmemit.c
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@@ -79,7 +79,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2"));
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ajFmtPrintAppS(&cmd, " --seed %d ", seed);
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if(a)
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ajStrAppendC(&cmd, " -a ");
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--- a/src/ehmmfetch.c
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+++ b/src/ehmmfetch.c
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@@ -74,7 +74,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2"));
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if(nhmm)
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ajStrAppendC(&cmd, " -n ");
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/* Note the output redirected to outfname */
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--- a/src/ehmmindex.c
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+++ b/src/ehmmindex.c
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@@ -68,7 +68,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex"));
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+ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2"));
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ajStrAppendC(&cmd, ajFileGetNameC(database));
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--- a/src/ehmmpfam.c
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+++ b/src/ehmmpfam.c
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@@ -122,7 +122,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2"));
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if(nuc)
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ajStrAppendC(&cmd, " -n ");
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ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z);
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--- a/src/ehmmsearch.c
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+++ b/src/ehmmsearch.c
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@@ -102,7 +102,7 @@
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iii.HMMER 'options' (that don't appear in ACD file)
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iv. HMMER & new parameters.
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*/
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- ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch"));
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+ ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2"));
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ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z);
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if(compat)
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ajStrAppendC(&cmd, " --compat ");
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