From fbe3c1e0b3175f7bf838bd93182a7bcbb4c67e9a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 23 Sep 2011 19:00:19 -0400 Subject: [PATCH] Adding warning on HardClipping Hard Clipping is still under heavy development and should not be used by anyone less prepared than MacGyver. --- .../sting/utils/clipreads/ClippingRepresentation.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java index 0dbe55726..d574ba2f0 100644 --- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java +++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingRepresentation.java @@ -21,6 +21,8 @@ public enum ClippingRepresentation { SOFTCLIP_BASES, /** + * WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED. + * * Change the read's cigar string to hard clip (H, see sam-spec) away the bases. * Hard clipping, unlike soft clipping, actually removes bases from the read, * reducing the resulting file's size but introducing an irrevesible (i.e.,