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clearing up a bit of confusion regarding the usage sequence hash. usa…

…ble sequences are sequences in the intersection of the two input maf files.
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1 parent b809f11 commit 9c48312a85065e44e9e5aa3637070c5f63878d2e @dentearl committed Apr 13, 2012
Showing with 4 additions and 4 deletions.
  1. +2 −2 mafComparator/README.md
  2. +2 −2 mafComparator/src/mafComparator.c
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@@ -44,7 +44,7 @@ in A.
###Options
* <code>mafComparator, version 0.3</code>
* <code>-a --logLevel</code> : Set the log level. [off, critical, info, debug] in ascending order.
-* <code>-b --mafFile1</code> : The location of the first MAF file (used to create sequence name hash.)
+* <code>-b --mafFile1</code> : The location of the first MAF file. If comparing true to predicted alignments, this is the truth.
* <code>-c --mafFile2</code> : The location of the second MAF file
* <code>-d --outputFile</code> : The output XML formatted results file.
* <code>-e --sampleNumber</code> : The number of sample homology tests to perform (total) [default 1000000].
@@ -60,4 +60,4 @@ Two mafs are included in the example/ directory and can be compared using the co
<code>$ mafComparator --mafFile1 example/a.maf --mafFile2 example/b.maf --outputFile comparison_a-b.xml</code>
-You may note in the output that there are no comparisons for the sequences that are found only in b.maf, i.e. sequences D, E and F. The hash of sequence names used for comparisons is populated using the --mafFile1 input. Sequences that only appear in the --mafFile2 input are ignored.
+You may note in the output that there are no comparisons for the sequences that are found only in b.maf, i.e. sequences D, E and F. The hash of sequence names used for comparisons is populated using the intersection of the sequence names from the --mafFile1 and --mafFile2 inputs. Sequences that only appear in --mafFile1 or only appear in --mafFile2 input are ignored.
@@ -176,8 +176,8 @@ void usage() {
"-a --logLevel : Set the log level. [off, critical, info, debug] "
"in ascending order.\n");
fprintf(stderr,
- "-b --mafFile1 : The location of the first MAF file (used to "
- "create sequence name hash.) If comparing true to predicted "
+ "-b --mafFile1 : The location of the first MAF file. "
+ "If comparing true to predicted "
"alignments, this is the truth.\n");
fprintf(stderr, "-c --mafFile2 : The location of the second MAF file. "
"If comparing true to predicted "

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