From: Michael R. Crusoe <crusoe@debian.org>
Subject: fix spelling typos found by Debian's Lintian check
Forwarded: https://github.com/macs3-project/MACS/pull/754
--- macs.orig/bin/macs3
+++ macs/bin/macs3
@@ -234,7 +234,7 @@
     group_output.add_argument("--verbose", dest="verbose", type=int, default=2,
                               help="Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2")
     group_output.add_argument("--trackline", dest="trackline", action="store_true", default=False,
-                              help="Instruct MACS to include trackline in the header of output files, including the bedGraph, narrowPeak, gappedPeak, BED format files. To include this trackline is necessary while uploading them to the UCSC genome browser. You can also mannually add these trackline to corresponding output files. For example, in order to upload narrowPeak file to UCSC browser, add this to as the first line -- `track type=narrowPeak name=\"my_peaks\" description=\"my peaks\"`. Default: Not to include trackline.")
+                              help="Instruct MACS to include trackline in the header of output files, including the bedGraph, narrowPeak, gappedPeak, BED format files. To include this trackline is necessary while uploading them to the UCSC genome browser. You can also manually add these trackline to corresponding output files. For example, in order to upload narrowPeak file to UCSC browser, add this to as the first line -- `track type=narrowPeak name=\"my_peaks\" description=\"my peaks\"`. Default: Not to include trackline.")
 
     group_output.add_argument("--SPMR", dest="do_SPMR", action="store_true", default=False,
                               help="If True, MACS will SAVE signal per million reads for fragment pileup profiles. It won't interfere with computing pvalue/qvalue during peak calling, since internally MACS3 keeps using the raw pileup and scaling factors between larger and smaller dataset to calculate statistics measurements. If you plan to use the signal output in bedGraph to call peaks using bdgcmp and bdgpeakcall, you shouldn't use this option because you will end up with different results. However, this option is recommended for displaying normalized pileup tracks across many datasets. Require -B to be set. Default: False")
--- macs.orig/docs/source/docs/broadPeak.md
+++ macs/docs/source/docs/broadPeak.md
@@ -52,7 +52,7 @@
 line will be necessary while uploading the broadPeak file to UCSC for
 display. Therefore, if you plan to upload the broadPeak file, either
 you turn on `--trackline` option in corresponding MACS3 subcommands,
-or add the trackline mannually to the beginning of the file. A minimal
+or add the trackline manually to the beginning of the file. A minimal
 trackline is like:
 
 `track type=broadPeak name="track name" description="track description"`
--- macs.orig/docs/source/docs/callpeak.md
+++ macs/docs/source/docs/callpeak.md
@@ -189,7 +189,7 @@
   MACS3 will include the trackline in the header of output files,
   including the bedGraph, narrowPeak, gappedPeak, BED format files. To
   include this trackline in the header is necessary while uploading
-  them to the UCSC genome browser. You can also mannually add these
+  them to the UCSC genome browser. You can also manually add these
   trackline to corresponding output files. For example, in order to
   upload narrowPeak file to UCSC browser, add this to as the first
   line -- `track type=narrowPeak name=`"my_peaks`" description=\"my
--- macs.orig/docs/source/docs/gappedPeak.md
+++ macs/docs/source/docs/gappedPeak.md
@@ -70,7 +70,7 @@
 line will be necessary while uploading the gappedPeak file to UCSC for
 display. Therefore, if you plan to upload the gappedPeak file, either
 you turn on `--trackline` option in corresponding MACS3 subcommands,
-or add the trackline mannually to the beginning of the file. A minimal
+or add the trackline manually to the beginning of the file. A minimal
 trackline is like:
 
 `track type=gappedPeak name="track name" description="track description"`
--- macs.orig/docs/source/docs/narrowPeak.md
+++ macs/docs/source/docs/narrowPeak.md
@@ -58,7 +58,7 @@
 line will be necessary while uploading the narrowPeak file to UCSC for
 display. Therefore, if you plan to upload the narrowPeak file, either
 you turn on `--trackline` option in corresponding MACS3 subcommands,
-or add the trackline mannually to the beginning of the file. A minimal
+or add the trackline manually to the beginning of the file. A minimal
 trackline is like:
 
 `track type=narrowPeak name="track name" description="track description"`
